Biometry in plant breeding

ARTICLE

Biometry in plant breeding Crop Breeding and Applied Biotechnology

21(S): e380621S5, 2021
Brazilian Society of Plant Breeding.
Cosme Damião Cruz1*, Pedro Crescêncio Souza Carneiro1 and Printed in Brazil
Leonardo Lopes Bhering1 http://dx.doi.org/10.1590/1984-
70332021v21Sa18

Abstract: In this manuscript we discuss the purpose and scope of biometry and
its interactions, complementation, and even overlap with several other areas
of genetics. We emphasize that biometry is an area of genetics that enables
researchers to analyze, process, and interpret biological phenomena from data,
usually obtained from experimental tests, in an improved way to guide strate-
gies and decision making for optimization of resources. We also highlight the
importance of the biometry professional in the context of breeding and the need
for continual training, due to new demands for and challenges from inclusion of
different types of information for processing and analysis paradigms to better
interpret these paradigms.
Keywords: Biometry, genetics, breeding, data analysis, quantitative genetics.

INTRODUCTION
Challenges have arisen from an increase in the demand for food because of
population growth and difficulties in increasing production through the costs
and adversities of climate change. These challenges are quite evident and have
required the use of extensive technical, human, and financial resources in the
attempt to overcome them. It is necessary to produce greater amounts of food
with quality, at low cost, and under increasingly diverse environmental conditions.
Breeding has a long history and was for many years practiced by ancestors
who had the ability and art of identifying individuals of superior performance,
and they passed traits on to new crops through the descendants of these
individuals. The success of this strategy certainly depended on the ability of
those dedicated and competent farmers who often adopted subjective and not
very accurate criteria in their choices, based on what was pleasing to the eye
and had good flavor. As time went on, breeding became more intensive and
included the need for always overcoming barriers and achieving new levels of
production (Allard 1971). This purpose required an intense effort of educating
professionals able to exercise the activity of breeders and act in public and *Corresponding author:
private institutions exclusively dedicated to the activity of breeding. Choosing E-mail: cdcruz@ufv.br
good genotypes was no longer an amateur activity but became a professional ORCID: 0000-0003-3513-3391
one; it was no longer exclusively an art, but came to be a science formed within
Received: 26 April 2021
the principles of genetics and experimentation. Observation was subjected to Accepted: 10 May 2021
the critique of accuracy and suitability for making decisions. Published: 06 July 2021
From Mendel’s laws, we discovered how the factors responsible for inheritance 1
Universidade Federal de Viçosa (UFV), De-
of the simplest traits were transmitted; however, many questions still remained partamento de Biologia Geral, Campus UFV,
regarding the mechanism of inheritance of more complex characteristics, such 36.570-900, Viçosa, MG, Brazil

Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021 1

CD Cruz et al.

as those involved in production of meat, milk, grain, or fruit, among other products. Therefore, a specific area in genetics
arose to deal with this matter, which was quantitative genetics, that is, an area that deals with inheritance and variation
of quantitative traits, which are strongly affected by the environment (Hallauer and Miranda Filho 1988, Vencovsky 1987,
Vencovsky and Barriga 1992, Falconer and Mackay 1996). This area was the precursor of biometry.
From the postulates of quantitative genetics, we began to understand how genetic and environmental factors interact
in control of these complex traits, and we came to understand the enormous difficulty faced by breeders in the process
of choosing and discarding genetic material. These choices are based on prediction of real genetic values of individuals
in competition, whether through the action of the environment, the genotype × environment interaction, or even
some genetic effects that hinder the selection process, such as dominance and epistasis effects. These factors hinder
establishing a good relationship between good performance of an individual (plant or animal) and the good quality of
their gametes, which are the biological links passed from one generation to another.
Quantitative genetics has made an enormous contribution, generating valuable information placed at the service of
breeders to obtain superior plants and animals in a shorter time and with fewer requirements of physical and financial
resources. All this information was obtained from costly experimental trials, conducted in a careful manner, which always
adopted and observed the scientific criteria of experimentation (Ramalho et al. 1993, Souza Júnior 2001, Oliveira et
al. 2005). The large amount of data and the need for more appropriate analyses of this information came to require a
new area of science, which meant the need for a new knowledge concentration area and a new contingent of qualified
professionals. This new area is called “biometry”, and the professionals acting in this area are called “biostatisticians”.
Within this perspective, many groups of researchers perceived that they could provide a more robust format to the
area of biometry, effectively contributing to dissemination of knowledge and training of professionals in the area, leading
to scientific advances from the proposal and refinement of quantitative methods for data analysis and interpretation
of genetic parameters.
We now understand biometry as the area of genetics that allows analysis, processing, and interpretation of biological
phenomena from data, generally obtained from experimental trials in a more refined manner, to direct strategies and
decision making for optimization of resources.
In the process of data analysis, the biometric area presents and refines models (in the case of statistical procedures)
and computational architecture (in the case of computational intelligence approaches) for better data processing. By
the action of data processing, biometry deepens studies on effective computational algorithms that make the use of
quantitative methods viable and generate information useful for interpretation of results. Because of its interpretive
activity, biometry requires knowledge of all biological areas, especially quantitative genetics, allowing understanding of
biotic and abiotic factors that affect the phenomenon studied and directing the choice of better strategies and decisions
aiming at optimal use of physical, financial, and human resources.

BIOMETRY AND QUANTITATIVE GENETICS – SCOPE AND COMPLEMENTARITY

One of the main objectives of breeding for crop and livestock production is an increase in yield, along with improved
nutritional quality of individuals (animals or plants) primarily directed to consumption. Such objectives can be achieved
through improving environmental conditions or through improving the genetic potential of individuals or populations
(Bernardo 2002, Borém et al. 2017).
By changing the environmental and technological conditions, it is possible to increase yield and advance other benefits,
because such changes allow the individual, plant or animal, to take better advantage of more favorable environmental
conditions. Various branches of knowledge contribute to improvements in the environment. In addition, improving the
genetic value of plants and animals contributes to achieving the desired aims. Most species have wide genetic diversity,
and it is possible to select and recombine more adapted, better quality, and more efficient genetic types.
In many situations, breeding is the only means of attaining increases in yield and quality and, in relation to techniques
of an environmental nature, it has the advantage of bringing about hereditary changes, that is, it is able to transmit
the phenotypes of traits of interest to descendants. Thus, in many cases, the agronomic or livestock advantages can be
perpetuated. In contrast, environmental improvement is normally quite costly and sometimes is not widely adopted

2 Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
Biometry in plant breeding

because of technical, personnel, and financial problems, and it may only provide good results if the genetic material
available is improved in a way to be able to express its full potential within the adequate environmental conditions. In
general, the researcher should be concerned with the combination of environmental and genetic improvement.
Professionals need to have a holistic view regarding breeding and environmental balance. Competent and qualified
actions depend on aggregating scientifically based knowledge with practical experience and a global vision that will lead
to satisfactory results. An understanding of the trait under selection and the instruments of generating information that
will guide decision making is fundamental. In this context, training professionals in genetic areas, especially quantitative
genetics and biometry, is indispensable.
Quantitative genetics is the part of genetics that studies quantitative traits, emphasizing their inheritance and the
components that determine their variation. Quantitative traits are generally controlled by various genes and are highly
affected by the environment, thus exhibiting continuous (and sometimes discontinuous) variations. Qualitative traits,
however, have simpler inheritance (conditioned by one or few genes) and are little or not affected by the environment
(Falconer and Mackay 1996). Biometry is complementary, because it pervades areas such as modeling, experimentation,
and computational processing to generate information that, illuminated by the theories of quantitative genetics, allows
interpretation of phenomena and decision making.
The study of inheritance and of variation in qualitative traits is based on analysis of generations, separating individuals
in classes and evaluating their proportions in the results of determined crosses. Nevertheless, information on the individual
is not of great value in the study of inheritance of quantitative traits, due to the random effect of the environment. If
the effect of the environment can both increase and diminish the phenotypic manifestation of a trait, the mean value
of a set of individuals will be a more reliable measurement, because the effects of the environment tend to cancel each
other out. Thus, quantitative traits are studied at the population level. In addition to the mean, another measure used
to define a population is the variance. Therefore, in studying quantitative traits, we evaluate which fractions of the
mean and of the variance are inheritable.
Measurements of central position and of dispersion are routinely dealt with in statistical analyses; however,
understanding regarding the mean and genotypic variance is a matter of great importance in the context of both
quantitative genetics and biometry. In quantitative genetics, we seek to understand and interpret the meaning of values
from this information for the breeder, whereas in biometry, we seek to establish the models that allow better estimation
of these values based on experimentation and observance of the laws of genetics.
We know, in a very simple way, that the mean represents the sum of all observations divided by their total number. In
some areas, this is sufficient. In quantitative genetics, the concern is not necessarily knowing how to estimate the mean,
but understanding its value when obtained in whatever population or in a population in Hardy-Weinberg equilibrium.
Breeders have clear expectations of the consequences regarding a mean derived from self-fertilization of a population
or regarding a cross between populations. Thus, important concepts emerge regarding inbreeding depression and
regarding heterosis that transcend the process of obtaining such estimates.
Understanding of the genotypic variation of a population calls attention to the existence of two basic models of
genetics. In one model, the genotypic value of an individual is predicted by the quantity (2, 1, or 0 alleles) of a favorable
allele found in the individual. In another model, this genotypic value refers to the consequence of the union of maternal
and paternal gametes, with different genetic information, that combine in fertilization. The decomposition of this
genotypic variation in additive variation and variation due to dominance in a monogenic model, and an epistatic variation
component when considering more than one locus, is fundamental for directing breeding programs based on sexual
recombination of the selected individuals and predicting the heterotic potential of hybrid combinations between superior
and divergent parents. From the perspective of biometry, the question of estimation is also fundamental, because correct
estimation and adequate interpretation are attributes of this area. Nevertheless, biometry also aggregates statistical
information, such as concepts of fixed and random effects, and information regarding statistical and genetic designs and
breeding strategies, especially those referring to the definition of testing and recombination units. From this, a more
appropriate value of genotypic variation can be obtained, which, elucidated by quantitative genetics, will be interpreted
and made available for breeders to use in breeding programs. Thus, as an illustration, genotypic variance in the context
of quantitative genetics can be expressed through the following equation:

Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021 3

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
CD Cruz et al.

σ2G = a2[(D+R) – (D–R)2] + d2H(1 – H) –2adH (D – R) (1)

for any population that has the genotypes AA, Aa, and aa with D, H, and R frequency and genotypic values μ + a,
μ + d, and μ – a, respectively, and
σ2G = 2pqα2 + (2pqd)2 (2)
for a population in Hardy-Weinberg equilibrium with the frequency of the A e a alleles given by p and q, respectively.
In this expression, α is the mean effect of gene replacement, given by ∝ = a + d(q – p).
While the expression σ2G has genetic interpretations, its estimator requires knowledge from the researcher that
goes beyond genetics, and therefore involves themes permeated by biometry. Thus, considering a genetic design of
analysis of generations that includes the P1 and P2 parent generations, which are homozygotes and contrasting, and the
derived F1 and F2 populations, there is the estimator of σ2G obtained through the information of variation measured in
the populations evaluated using the following equation:
V(P1)+V(P2)+2V(F1)
σ̂ 2G = V(F2) – (3)
4
However, if the population is structured in families and evaluated in a statistical design, such as randomized or
completely randomized blocks, the estimator of σ2G would depend on information of an analysis of variance referring
to the treatment mean squares (MST), residual mean squares (MSR), and mean squares of the number of replications
of each family in the design, that is
MST - MSR
σ̂ 2G = (4)
r
Thus, from the data of experimentations and from the basic principles of biometry, along with knowledge of the
breeding objectives, biometry allows us to obtain information regarding the genetic variability of the population using
equations 3 and 4, which will provide valuable interpretations according to the expressions, just as described in equations
1 and 2.
Another type of information that is essential in breeding is gain from selection (GS), the result of careful and meticulous
activity of the breeder in identifying the best genotypes and recommending them for recombination, generating the
improved population (Paterniani 1996). Quantitative genetics deals with this matter by affirming that the GS is the
consequence of the displacement of the genotypic mean, since individuals that carry favorable alleles through the action
of the breeder have a greater chance of leaving descendants than others do. With the practice of selection, the mean
of a population for a determined trait of interest will be given by
μs = μ0 + GS
where μs is the mean value of the improved population; μo is the original mean of the population; and GS is the gain
obtained from selection. Considering that both the original population and the improved population are in Hardy-Weinberg
equilibrium, if the frequency of the favorable allele in the improved population is p' = p + Δp, the mean values of the
populations in question will be given by
μ0 = μ + (2p – 1)a + 2p(1 – p)d
and
μs = μ + (2p' – 1)a + 2p'(1 – p')d
Thus, so that the value of μs is superior to μo, resulting from the use of a selection technique, the values of gain from
selection (GS) must be expressive. These gains depend on the genetic structure of the population and on the genetic
effects of the alleles that control the trait under selection. In general, there are difficulties in knowing the values of gene
frequency, as well as the genetic effects in a determined population. However, estimation of additive variance, based
on appropriate genetic and statistical designs, will enable the prediction of said gain.
Assuming that for selection of quantitative traits, the value of Δp (given by p' – p) is expected to be small and that,
consequently, its quadratic value (Δ2p) can be considered null, the equation is

4 Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
Biometry in plant breeding

GS = 2Δp [a + d(1 – 2p)] =2∆pα (5)

Thus, it is understood by quantitative genetics, based on equation 5, that the increase in the mean of a population,
through selection, is directly proportional to the variation in the gene frequency imposed by the practice of selection
and to the value of exchange between the alleles given by the mean effect of gene replacement (∝). Expression 5 in
itself is interpretable, but it may also give rise to other relevant information, such as the fact that the GS will essentially
depend on the magnitude and the significance of the additive variance component, which, for its part, is a quadratic
function of ∝.
A complementation of the interpretation of the definition of the GS can be obtained by the biometric area, considering
aspects of the trait, of the experimentation, and of the selection techniques, among others. Thus, we can understand
the gain from selection by means of the following expression:
GS = H2DS (6)
where H2 is the heritability of the trait and DS is the differential of the selection carried out, expressed by the difference
between the mean values of the individuals selected and of the original population under selection. A more extensive
manner of interpretation is the expansion of expression 6, which results in the following equation:
GS = ip σGH (7)
By equation 7, we find that the GS is the consequence of some factors that go beyond genetic factors. Thus, we can
visualize that it is dependent on the intensity of the selection carried out; as it grows, it can lead to greater increases
in gains, but it is known that it can lead to loss of variability in future generations through reduction in the effective
size of the population under selection. It will depend on the breeding arrangement adopted, expressed by the parental
control (p), where different units of selection and of recombination may be involved. It will depend on selective
accuracy (expressed by H, which is the square root of heritability), indicating that well-conducted experimental trials
and adoption of replications and appropriate designs may favor the GS. Finally, there is the need for genetic variability
(σG, which expresses the genotypic standard deviation) to have gains from selection. The conclusion is that expressions
5, 6, and 7 are interpretations of the same phenomenon (GS) from different angles. Nevertheless, the main point here
is to affirm that there is no interest in establishing that they are subjects from different areas, but rather that we can
complement, deepen, and diversify knowledge to enrich our information and better support our decision making when
areas complement each other.
Heterosis is defined as the superiority of the descendant in relation to the mean of its parents. If this definition is
treated on the basis of quantitative genetics, we can consider two populations, P1 and P2, in Hardy-Weinberg equilibrium,
with genotypic means given by the following equations:
μ1 = a(p – q)+ 2pqd
μ2 = a(p' – q')+ 2p'q'd
The genotypic mean of the F1 population will be given by
μF1 = ap(p – ∆) + d[2pq + ∆(p – q)] – a[q(q + ∆)]
Thus, heterosis (h) is given by

h = μF1 – μp = μF1 – μ1 + μ 2 = d∆2 (8)

2
From expression 8, it can be concluded that the heterosis manifested in intervarietal hybrids is directly in accordance
with the genotypic value of the heterozygote (d), expressed by the mean degree of dominance and of the difference in
gene frequency, that is, of genetic diversity between the populations crossed. It is also understandable that heterosis
will be at a maximum when one allele is fixed in one population and the other in the other population, as well as that
if the populations do not differ in gene frequency, there will be no heterosis. Many studies of evaluation of genetic
diversity among parents have been substantiated based on this expression, seeking those of good performance and that
exhibit diversity, recommending their crosses with the expectation that the hybrid will manifest heterosis and that the
segregating populations will show variability and transgressive individuals. Quantitative genetics stimulates researchers

Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021 5

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
CD Cruz et al.

to seek better understanding regarding heterosis, presenting and discussing some hypotheses of dominance and/or
overdominance that would explain the appearance of heterosis. Furthermore, biometry takes the route of modeling
and, as in the studies of diallel analysis proposed by Gardner and Eberhart, presents us with concepts and estimators
of mean, varietal, and specific heterosis that are very useful in a program that aims to recommend hybrid combinations
for commercial growing.
Finally, we emphasize one of the most important items of information in breeding, which is heritability. Quantitative
genetics invites us to an understanding of this phenomenon from different equally important angles. We can understand
heritability as being the proportion of phenotypic variation (σ2F) that has a genetic nature and indicates the degree
of difficulty in obtaining gains from selection in accordance with the existence of genuinely genetic variability in the
population of interest.
σ²G
H2 = σ²F
(9)
Yet, heritability is also a measure of the accuracy of the selection process, indicating the degree of accord between
the phenotypic value manifested by the individual and its true genetic value. Thus, heritability can be quantified by the
square of the correlation between observable phenotypic values and true genotypic values, that is
H2 = r2FG (10)
where F = G + M, in which the phenotypic value (F) is given by the genotypic value (G) under the effect of the medium
(M). In expression 10, it is assumed that cov (F, G) = σ2G , since replication and experimental randomness and random
action of the environment ensure that the association between genotype and environment is null.
A third equally important concept refers to the fact that heritability measures how much the variations of the parents
are reflected in the variations passed on by descendants. In this context, a linear relation is established between the
genetic values predicted and manifested in the progeny (F) and the phenotypic values manifested in its parents (P), that is
F = β0 + βPFP + ε
Thus,
H2 = βPF (11)
Finally, a widely used concept is that which relates the genotypic performance of the individuals of an improved
population (Y) resulting from the recombination of superior individuals, identified in comparative tests between
individuals of an original population under selection, manifesting phenotypic values (X). In this case, the following
predictive model is used:
(Y – Y�) = β̂(X – X�)
where (Y – Y�) is the gain from selection in the selected progeny and (X – X�) is the differential of selection practiced in
the population under breeding. Also,
H2 = β̂ = βUt,Um (12)
where βUt,Um is the regression coefficient established by the relation between the phenotypic values of the test unit (Ut)
and the genotypic values of the improved unit (Um).
We see that the definitions presented in expressions 9 to 12 are genetically based and are closely related to the
questions of breeding. However, obtaining the value of this heritability requires a great deal of other information,
such as type of family, genetic and statistical design, replications, breeding strategies, and others. Thus, supposing the
evaluation of a set of g families in randomized block experiments with b blocks, in which n plants were evaluated per
plot, the biometric approaches that take into consideration all the genetic aspects, as well as the information of the
breeding strategy adopted and experimental particularities, would allow estimation of different heritability coefficients
from the same experiment. These coefficients are not only interpreted under the standards of quantitative genetics, but
also meet the different requirements of the breeder in decision making, such as how to adopt selection between and
within a family, or stratified selection, combined selection, or simply family selection, among others.

6 Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
Biometry in plant breeding

BIOMETRY – KNOWLEDGE GUIDING THE SELECTION STRATEGY

Breeding programs require intensive experimentation so that accurate genetic values can be obtained and used
as selection criteria. This has been a major challenge for breeders, that is, recognizing which evaluated items will
have the best per se performance or that will provide the best descendants in segregating generations. In the early
days of breeding, the individual phenotypic information was taken as the indirect value of the genotype; however,
quantitative genetics has shown that most of this value, and especially most of the variation among these values,
could have an environmental cause, and the adoption of these values as a criterion could lead to selection that is
not very accurate, especially for polygenic traits strongly affected by the environment (Paterniani 1966, Falconer
and Mackay 1996).
The adoption of the basic principles of experimentation, such as the need to conduct trials with replication,
randomness, and, if necessary, local control, led to a revolution by providing more accurate mean values, information
regarding experimental accuracy, and estimates of genetic and environmental parameters useful in guiding breeding
strategies. This may have been the moment that the foundations of biometry emerged in breeding, in which there was
complementation between genetic and statistical principles for a common purpose.
Proposals for improvement in the information regarding individuals and populations have been presented through
diverse biometric approaches. For decades, questions regarding indirect selection, simultaneous selection, and family
selection were raised, studied, and substantiated. Thus, theories of correlated responses or selection indices have indicated
that aggregating information on auxiliary traits that are generally easier to measure and with greater heritability can
provide criteria that lead to more balanced gains in a set of traits of interest to breeders. Another approach is one that
seeks to increase selective accuracy through criteria that involve information on the individual, the focus of selection,
and of its kin, generating family indices. In this case, the experimentation and the information regarding the genealogy of
those evaluated become fundamental. Some genetic designs were especially established so that, in a single experiment,
information could be obtained on the individuals and their kin, such as diallel crosses and designs I and II of Comstock
and Robinson, in which the presence of both full sibs and half sibs are found. These designs provide information that
assists breeders in selection of parents seeking to obtain base (segregating) populations of greater potential, as well as
an understanding of the genetic effects involved in genetic control of the traits under study.
Along with the intra-allelic (dominance) and inter-allelic (epistasis) interactions, the genotype × environment interaction
(G×E) is among the three main genetic difficulties faced by the breeder. The biometric area provided modeling that
allowed a basis for better understanding of this G×E interaction, as well as alternatives to mitigate its harmful effects in
the selection of genotypes aiming at recommendation. In this phase, the analyses of environmental stratification and
studies on adaptability and stability are prominent. For these studies, various methodologies have been proposed, which
allow recommendation more suitable for a wide region or for specific conditions. However, from the perspective of
genotype selection aiming at recombination in recurrent selection programs, in which the effect of the G×E interaction
can be an advantage, biometry also responded with appropriate modeling, presenting selection indices that capitalize
on the G×E interaction (Cruz et al. 2011a, Cruz et al. 2012, Cruz et al. 2014).
The experimental statistics and biometry areas have contributed a large number of models, some of which achieve
complexity by their parametrization with the sole purpose of ensuring the good choice of genetic material and of
establishing a predicted value of performance of the individual or of its descendant in the best manner possible.
Processing these data has become viable by the availability of increasingly powerful computational resources and the
establishment of computational routines that incorporate the features of the biological phenomenon under study in
the statistical models.
More recently, breeding has aggregated additional information of great value for establishment of selection criteria.
Massive datasets of molecular markers, of spectroscopies, such as near infrared (NIR) imaging, and of images have allowed
much more parametrized models to be fitted, with substantial gains in measurements of quality of fit. However, the use
of models with datasets of large dimensions requires knowledge of more effective approaches and, for that purpose,
some basic principles of prediction through statistical paradigms, computational intelligence, machine learning, and
even non-Boolean logic are being incorporated in the biometric area (Cruz and Nascimento 2018).

Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021 7

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
CD Cruz et al.

THE BIOMETRIC AREA AS A RESPONSE TO ADVANCES IN THE AGE OF MOLECULAR GENETICS

Genetics is constantly evolving, overcoming new challenges and responding to the desires of the population regarding
the most varied themes, emphasizing some themes related to heredity and to genetic control of important traits. This
is also true in the biometric area. With the advent of modern molecular biological techniques, various methods have
arisen for detection of genetic polymorphism directly at the DNA level (Cruz et al. 2011b). As of that time in the 1980s,
this gave rise to a new cycle of knowledge generation, of fitting models, and development of algorithms appropriate
for data processing, with a view toward the need to aggregate these data to the values of a phenotypic nature that are
traditionally measured in plants and animals under selection.
It should be noted that this new information required new studies and scientific effort and resulted in advancement
both in breeding activities, with information from genetic mapping and detection of genes controlling quantitative traits
in plants and animals, and in analysis of population dynamics, with studies on diversity, regular mating systems, degree
of kinship, and others.
Groups that act in the biometric area responded to world demand and formulated new models and adapted or
refined procedures to aggregate the data and information coming from molecular genetics studies, which resulted in
valuable information, including the prediction of genomic values of unrealized individuals and hybrids. They also helped
clarify important phenomena, such as epistasis and hybrid vigor.
Among the areas of biometric study that involve the use of DNA molecular markers, the contributions in the strategy
of genome-wide selection (GWS) are noteworthy. It allows aggregation of DNA information in selection of superior
genotypes and provides greater genetic gains with greater effectiveness, lower cost, and time savings (Resende 2008,
Silva et al. 2015, Borém et al. 2017, Sant’Anna 2019a, Sant’Anna 2019b).
Genome-wide selection (GWS) has been adopted for the development of more accurate methods of prediction of
phenotypes of plants and animals, and to make inferences regarding their regulators (Meuwissen et al. 2001, Resende
2008). Although GWS is efficient, some challenges are routinely faced by professionals in the biometric area, which
include genetic questions inherent to the use of molecular markers, statistical questions regarding the use of different
data analysis paradigms, and especially computational questions arising from the requirement of analysis of relatively
large datasets.
Thus, we perceive the importance of having professionals with a wide vision and ability to associate themes from
areas such as the exact sciences and biological sciences to overcome great challenges, such as understanding genetic
polymorphism, gene linkage, gametic phase disequilibrium, and genetic control of traits, so that biological models can
be well established. Other challenges are in regard to presuppositions that must be assumed a priori to perform suitable
stochastic analyses and obtain good interpretation of results. In addition, researchers must be very careful in relation to
the dimensions of the model adopted (or parametrization), the presence of harmful effects of multicollinearity among
the markers (explanatory variables), and the complexity of the quantitative traits under study (response variables), for
which, without the assistance of appropriate computational resources, proposing or presenting solutions becomes
unfeasible. Fortunately, various biostatisticians have sought to solve genetic issues, overcome computational limitations,
and make analyses more viable and faster. They have endeavored to obtain accurate information regarding response
variables, adopt more robust methods, and make use of strategies that can accommodate the information available in
high dimensional molecular marker matrices.
Once more, we can highlight that the biometric area, applied to the questions of GWS, allows one to exercise the
full knowledge of models presented by quantitative genetics, the uses of which were simplified over the years; and
some effects known to be important, such as dominance and especially epistasis, were neglected. Thus, the possibility
of greater parametrization of GWS models contributing to advance information is also noteworthy since, most of
the time, additive or additive-dominance prediction models were used (Cruz et al. 2012, Cruz et al. 2014). In view of
that, the possible effects due to the intra- and interallelic interactions were not detected to be suppressing genetic
information and, in the statistical context, inflating the residue associated with the prediction model adopted. In this
context, biostatisticians presented new statistical models and sought new modeling alternatives, which have been used
in breeding programs (Gianola et al. 2011, Silva et al. 2014, Carneiro et al. 2017, Sant’Anna et al. 2019, Sant’Anna et al.

8 Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
Biometry in plant breeding

2021), and unlike the conventional stochastic modeling used up to then, they are based on the principles of machine
learning and computational intelligence (Silva 2014).
By incorporating the use of methodologies and the application of new paradigms to breeding, such as computational
intelligence and machine learning, biometry has provided new alternatives of analyses to assist in cultivar selection.
Artificial intelligence methods are rapidly becoming essential for data analysis, especially as a support for decision-
making processes (Carneiro et al. 2017).

THE BIOMETRIC AREA ADAPTED TO NEW PARADIGMS OF ANALYSIS AND DATA INTERPRETATION
Biometry applied to breeding is based on genetic principles and the purpose of meeting demands for interpretation
of biological phenomena and providing information that can guide strategies and optimize resources. Thus, processing,
data analysis, and interpretation of results is the activity inherent to the work of biostatisticians. The accumulation of
information and advance of new technologies, especially in the area of computation, has made the biometric area
attentive to new analysis techniques with diverse objectives, especially for analyses of prediction, classification, and
recognition of patterns (Resende 2002, Resende et al. 2014).
Biometry, like data science, has earned prominence worldwide. Both are interdisciplinary areas directed to the study
and analysis of data aiming at detection of patterns and/or obtaining information to assist in decision making. Biometry
differs by the type of data it uses, by the phenomena emphasized, and, essentially, by being practiced in total observance
of the principles of genetics and the purposes of breeding. In 2019, data scientists appeared in first place in the ranking
made by the American recruiting site Glassdoor, which lists the best jobs in the United States. Biostatisticians are part
of this select group of researchers.
Many statistical procedures summarize or allow interpretation of phenomena through measuring core trends,
generally represented by the mean (arithmetic, weighted arithmetic, geometric, and harmonic), median, and mode.
Their objective is to represent an entire set by a single value, and many hypotheses are associated with the existence
of equality of these means in different sources of variation. Another measurement often requested in statistical studies
refers to dispersion, represented by information regarding amplitude, variance, and standard deviation. Based on these
core measurements, we construct estimates of error of a study and analyze the dispersion of its data.
Statistical models attempt to explain a response variable, with the purpose of fitting or classification through
a set of variables or independent effects beyond an experimental error. Presuppositions regarding these errors
are necessary and indispensable for establishment of estimators that lead to values that will serve as a basis
for guiding strategies and adoption of procedures for optimization of resources. Biometric procedures based on
principles and statistical models are widely applicable in breeding. Nevertheless, other currents of thought have
been adopted, leading to solutions from different perspectives and giving researchers the opportunity to adopt
the solution of greatest interest.
Differentiated solutions for problems in the biometric area can be achieved within the area of artificial intelligence
(AI), or computational intelligence, which deals with automation of intelligent behavior and is divided into different
paradigms, notably the symbolic, connectionist, and evolutionary paradigms. The symbolic paradigm is based on symbolic
transformations (numbers, letters, words, and symbols) to establish a logical route until discovering a determined
solution. The most successful form of symbolic AI is specialist systems, which use a network of production rules. The
connectionist paradigm includes the procedures of neural networks and fuzzy logic inspired by the operation of the
human brain. The term was introduced by Donald Hebb in the 1940s. The essence of these procedures is the learning
algorithm that allows modification of the weights of connections and extraction of linear and non-linear information
from the problem under study; it is therefore of great interest to breeding. Finally, there is the evolutionary paradigm,
which is composed of a series of algorithms inspired by natural evolution, called genetic algorithms.
The neural network is an area of computational intelligence that meets the need for generating solutions related to
numerous problems, including those of classification and prediction, which are routine activities in breeding. In contrast
with the statistical approach, information is not summarized, but each example, or piece of information, is relevant in
a learning process in which each input (which corresponds to the independent variables in statistical vocabulary) has

Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021 9

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
CD Cruz et al.

weights, called adjustable synaptic weights. Among the types of neural networks important in solving classification
problems, the multilayer perceptron and radial basis function neural networks are prominent.
In neural networks with the purpose of fitting or classification, the variations in a response variable can be explained
by a set of inputs whose linear and non-linear actions are captured through abstract variables, with information
generated by neurons in hidden or intermediate layers with a variable number of both layers and neurons per layer.
Such potentialities allow analysis of complex traits in a more accurate manner and better understanding of important
phenomena such as dominance and epistasis.
Curently, biostatisticians make use of the resource of machine-learning approaches, which allow machines to
develop models and make predictions without the need for reprogramming. As the machines are exposed to new data,
they learn more and adapt in an independent manner. Machine-learning procedures can be classified as supervised or
non-supervised. In supervised learning, the algorithms learn which model is most suitable for predicting the variable
of interest, based on dependent variables (or inputs), through a set of examples that are submitted to the system. It
is said that this type of learning involves the participation of an “external agent” and is generally used in situations in
which the historic data foresee possible future occurrences. The decision tree procedure and its refinements and neural
networks are prominent in this type of learning. In unsupervised learning, the procedure generates response patterns
from measurements in variables of interest based on some structure and measure of similarity. The main procedures
are reduction of dimensionality (principal component analysis, multidimensional scaling), cluster analysis (K-means,
hierarchical methods), and Kohonen self-organizing maps.

CONCLUSION
Biometry is an area of genetics in continuous evolution, which has contributed to generating information and finding
solutions to diverse questions in genetics and breeding. The professional in this area must know the features of the basic
factors of heredity, population dynamics, mating systems, and strategies for conducting populations, among others. In
addition, (s)he must be attentive to all the tools of analysis and of data processing arising from the rapid and continuous
evolution of this area. It is an area that essentially depends on the critical perspective and attitudes of good breeders
that are data-generating agents and the great beneficiaries of the information generated, but their attentive eye is on
the methods of data analysis and on the algorithms that allow data processing supported by the biometric area.
A view of the current scenario leads to the conclusion that as many associated areas advance, an increasing volume
of data will become available, which will require careful analysis and interpretation. These data now also result from
the accumulation of information deposited in historical databases, and from aggregating and prospecting information of
diverse natures, involving data on genetic materials, climate, soil, etc. Also prominent in this scenario are globalization
of information and capturing of new data, especially acquisition and interpretation of image and spectral data.
There is an urgent need for further advances, now supported by biometric genetics, in the context of data processing
and in computational intelligence and machine-learning approaches. This is associated with emerging areas in breeding,
especially phenomics, and further developments in the question of handling big data.

REFERENCES Cruz CD and Nascimento M (2018) Inteligência computacional aplicada

ao melhoramento genético. Editora UFV, Viçosa, 414p.
Allard RW (1971) Princípios do melhoramento genético das plantas.
São Paulo, 485p. Cruz CD, Carneiro PCS and Regazzi AJ (2014) Modelos biométricos
aplicados ao melhoramento genético. Editora UFV, Viçosa, 668p.
Bernardo R (2002) Breeding for quantitative traits in plants. Woodbury,
Stemma, 368p. Cruz CD, Ferreira FM and Pessoni LA (2011b) Biometria aplicada ao estudo
da diversidade genética. Suprema, Visconde do Rio Branco, 620p.
Borém A, Miranda GV and Fritsche-Neto R (2017) Melhoramento de
plantas. 7th end, Editora UFV, Viçosa, 543p. Cruz CD, Regazzi AJ and Carneiro PCS (2011a) Modelos biométricos
aplicados ao melhoramento genético. Editora UFV, Viçosa, 514p.
Carneiro VQ, Silva GN, Cruz CD, Carneiro PCS, Nascimento M and
Carneiro JES (2017) Artificial neural networks as auxiliary tools for Falconer DS and Mackay TFC (1996) Introduction to quantitative genetics.
the improvement of bean plant architecture. Genetics and Molecular Longman Group Limited, Edinburgh, 464p.
Research 16: gmr16029500. Gianola D, Okut H, Weigel KA and Rosa GJ (2011) Predicting complex

10 Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions
Biometry in plant breeding

quantitative traits with Bayesian neural networks: a case study with seleção genômica no melhoramento de plantas. Novas Edições
Jersey cows and wheat. BMC Genetics 12: 87. Acadêmicas, Mauritius, 128p.

Hallauer AR and Miranda Filho JB (1988) Quantitative genetics in maize Sant’anna IC, Nascimento M, Silva GN, Cruz CD, Azevedo CF, Gloria LS
breeding. Iowa State University Press, Ames, 468p. and Silva FF (2019b) Genome-enabled prediction of genetic values
for using radial basis function neural networks. Functional Plant
Meuwissen THE, Hayes BJ and Goddard ME (2001) Prediction of total
Breeding Journal 1: a1.
genetic value using genome wide dense marker maps. Genetics
157: 1819-1829. Sant’anna IC, Silva GN, Nascimento M and Cruz CD (2021) Subset selection
of markers for the genome-enabled prediction of genetic values using
Oliveira AC, Furtado DF and Ramalho MAP (2005) Experimentação em
radial basis function neural networks. Acta Scientiarum. Agronomy
genética e melhoramento de plantas. UFLA, Lavras, 300p.
43: e46307.
Paterniani E (1966) Genética e melhoramento do milho. In Krug CA (ed)
Silva GN and Cruz CD (2015) Redes neurais artificiais: Novo paradigma
Cultura e adubação do milho. Instituto Brasileiro de Potassa, São
para a predição de valores genéticos. Schaltungsdienst Lnag o.H.G,
Paulo, p. 109-148.
Berlin, 92p.
Ramalho MAP, Santos JB and Zimmermann MJO (1993) Genética
Silva GN, Tomaz RS, Sant’anna IC, Nascimento, M, Bhering LL and Cruz CD
quantitativa em plantas autógamas: aplicações ao melhoramento
(2014) Neural networks for predicting breeding values and genetic
genético do feijoeiro. UFG, Goiânia, 271p.
gains. Scientia Agricola 71: 494-498.
Resende MDV (2002) Genética biométrica e estatística no melhoramento
Souza Júnior CL (2001) Melhoramento de espécies alógamas. In Nass LL,
de plantas perenes. Embrapa, Brasília, 975p.
Valois ACC, Melo IS, Valadares Inglis MC (org) Recursos genéticos e
Resende MDV (2008) Genômica quantitativa e seleção no melhoramento melhoramento de plantas. Fundação MT, Rondonópolis, p. 159-199.
de plantas perenes e animais. Embrapa Florestas, Colombo, 330p.
Vencovsky R (1987) Herança quantitativa. In Paterniani E and Viégas
Resende MDV, Silva FF and Azevedo CF (2014) Estatística matemática, GP (ed) Melhoramento e produção do milho. Fundação Cargill,
biométrica e computacional. Editora UFV, Viçosa, 881p. Campinas, p. 137-214.

Sant’anna IC and Cruz CD (2019a) Redes neurais artificiais na predição Vencovsky R and Barriga P (1992) Genética biométrica no
de valores genéticos: aplicação de inteligência computacional e fitomelhoramento. Revista Brasileira de Genética, Ribeirão Preto,
486p.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original work is properly cited.

Crop Breeding and Applied Biotechnology - 21(S): e380621S5, 2021 11

Downloaded from https://cabidigitallibrary.org by 103.174.4.168, on 10/11/24.
Subject to the CABI Digital Library Terms & Conditions, available at https://cabidigitallibrary.org/terms-and-conditions