HERITABILITY OF QUANTITATIVE CHARACTERS IN FARM ANIMALS

Heritability within groups is uninformative about differences among groups: Cases from behavioral, evolutionary, and statistical genetics

Without the ability to control or randomize environments (or genotypes), it is difficult to determine the degree to which observed phenotypic differences between two groups of individuals are due to genetic vs. environmental differences. However, some have suggested that these concerns may be limited to pathological cases, and methods have appeared that seem to give-directly or indirectly-some support to claims that aggregate heritable variation within groups can be related to heritable variation among groups. We consider three families of approaches: the "between-group heritability" sometimes invoked in behavior genetics, the statistic [Formula: see text] used in empirical work in evolutionary quantitative genetics, and methods based on variation in ancestry in an admixed population, used in anthropological and statistical genetics. We take up these examples to show mathematically that information on within-group genetic and phenotypic information in the aggregate cannot separate among-group differences into genetic and environmental components, and we provide simulation results that support our claims. We discuss these results in terms of the long-running debate on this topic.

Heritability within groups is uninformative about differences among groups: cases from behavioral, evolutionary, and statistical genetics

Without the ability to control or randomize environments (or genotypes), it is difficult to determine the degree to which observed phenotypic differences between two groups of individuals are due to genetic vs. environmental differences. However, some have suggested that these concerns may be limited to pathological cases, and methods have appeared that seem to give-directly or indirectly-some support to claims that aggregate heritable variation within groups can be related to heritable variation among groups. We consider three families of approaches: the "between-group heritability" sometimes invoked in behavior genetics, the statistic P S T used in empirical work in evolutionary quantitative genetics, and methods based on variation in ancestry in an admixed population, used in anthropological and statistical genetics. We take up these examples to show mathematically that information on within-group genetic and phenotypic information in the aggregate cannot separate among-group differences into genetic and environmental components, and we provide simulation results that support our claims. We discuss these results in terms of the long-running debate on this topic.

Morphological Diversity and Genetic Parameter of Okra (Abelmoschus esculentus L. Moench) Genotypes

<b>Background and Objective:</b> Considering that the potential for okra as an anti-diabetic is very high, while okra productivity in Indonesia is still low, a plant breeding program through variety development is needed. One of the initial activities that needs to be carried out is the characterization of various genotypes, both quantitative and qualitative characters. This research aimed to obtain information on the diversity of morpho-agronomic characters in okra genotypes. <b>Materials and Methods:</b> The experiment was conducted as a randomized block design, one factor is genotype with three replications. The materials used in this research were 20 okra genotypes. The experimental units used in this research were 60 units. Each experimental unit consists of 10 sample plants. Analysis of quantitative character variations used PKBT-STAT 3.1. Cluster analysis was carried out with PBSTAT-CL 2.1.2 with the Gower dissimilarity and average linkage clustering methods. Furthermore, analysis was carried out using SAS OnDemand for Academics to see the distinguishing characteristics between clusters. <b>Results:</b> There were differences in okra genotypes based on qualitative and quantitative characteristics. The most diverse quantitative character is the yield component, which is the fruit character. Variance in genetic and heritability showed broad and high criteria, respectively. Based on cluster analysis results, okra genotypes were grouped into 3 clusters with a cophenetic distance value of 0.40. Cluster 1 consists of 9 genotypes. Cluster 2 consists of 10 genotypes. Cluster 3 consists of 1 genotype the Red Hill Country genotype. The grouping in cluster analysis was carried out based on leaf width, number of fruits, fruit weight, fruit diameter and carpel thickness character. <b>Conclusion:</b> This diversity of okra germplasm can facilitate plant breeding activities in the future by selecting genotypes to serve as parents according to the objectives carried out.

Genetic diversity, transcript heterogeneity and allele mining of TaSKP1-6B-4 gene variants across diverse genotypes under terminal heat stress and genome wide characterization of TaSKP1 gene family from bread wheat (Triticum aestivum L.)

SKP1 (S-phase kinase protein1) is an essential regulatory component of SCF (Skp1-cullin-F-box) E3 ubiquitin ligases involved in maintenance of cellular protein homeostasis through ubiquitin mediated proteasome system (UPS). UPS play a key role in stress response and grain yield. Earlier, we isolated TaSKP1-6B-4, highly induced in flag leaf tissues (Accession No. KJ830759.1) of developing wheat caryopses under heat stress. To further assess the functional role of SKP1, genetic variability analysis was carried out in a panel of 25 contrasting germplasm through extensive phenotyping and transcript profiling of TaSKP1-6B-4 during anthesis under ambient and terminal heat stress (THS) in field experiments for two consecutive years. The analysis of variance revealed significant variations for all the traits studied. Higher H2(%), GCV, PCV, GA and GA% mean observed in tiller number per plant (23.81, 17.65, 5.71, 28, 30.86%) and grain number per head (30.27, 82.79, 60.16, 105.00, 108.64%) under THS over ambient temperature. Higher fold induction of TaSKP1-6B-4 transcripts was recorded in 10 genotypes viz. HD2967 (9.9), IC145456 (6.18) in flag leaf; while C-306 (15.88), RAJ3765 (8.37) in ear head. Allele mining of SKP1-6B-4 showed genotypic sequence variations. Whole genome wide search of SKP1 gene family identified 95 SKP1 genes which were structurally characterized. Grain yield, leaf senescence and other agronomic-morpho-physiological parameters combined with transcript profiling, cvHD2967, was found to be the best positively responsive to THS which by pedigree was not heat tolerant. We report a novel 2 year comprehensive field based analysis on collective genetic variability and SKP1/UPS modulation under a natural environmental setting. The data reveals potential functional role of UPS under THS and tolerant cultivars can be further utilized for clarifying the role of UPS mechanistically at the molecular level and for developing terminal heat stress tolerant wheat.

Evaluation of yield attributes and bioactive phytochemicals of twenty amaranth genotypes of Bengal floodplain

Twenty vegetable amaranth (VA) genotypes were evaluated to assess the variability, associations, path coefficient, and principal component analysis (PCA) of morpho-chemical traits. The genotypes exhibited adequate antioxidant colorants, phytochemicals, and antiradical capacity with significant variations across genotypes. Genetic parameters revealed selection criteria for the majority of the traits for improving amaranth foliage yield (FY). Based on correlation coefficient, stem weight, stem base diameter, root weight, plant height, and shoot weight for significant development of FY of VA. Observing significant genotypic correlation with high positive direct effects on FY, the path coefficient (PC) of root weight, stem base diameter, stem weight, and shoot weight could contribute to the noteworthy development of FY of VA. The genotypes AA5, AA6, AA8, AA10, AA11, AA19, and AA20 might be selected for high FY, antioxidant colorants, and antiradical phytochemicals to utilize as colorants and antiradical rich superior high yielding cultivars. The first PC accounted for 37.8% of the variances, which implies a larger proportion of variable information explained by PC1. The features that contributed more to PC1 were FY, SW, STW, RW, and PH, whereas Chl b, total Chl, and Chl a contributed to the second PC. This suggests that there are significant genetic differences between amaranths in terms of biochemical and agro-morphological characteristics. The findings of the current work support plant breeders to investigate the genetic potential of the amaranth germplasm, notably in biochemical parameters. High colorants enrich genotypes that can be selected for extracting natural colorants to use in food processing industries.

Genomics in animal breeding from the perspectives of matrices and molecules

BACKGROUND

This paper describes genomics from two perspectives that are in use in animal breeding and genetics: a statistical perspective concentrating on models for estimating breeding values, and a sequence perspective concentrating on the function of DNA molecules.

MAIN BODY

This paper reviews the development of genomics in animal breeding and speculates on its future from these two perspectives. From the statistical perspective, genomic data are large sets of markers of ancestry; animal breeding makes use of them while remaining agnostic about their function. From the sequence perspective, genomic data are a source of causative variants; what animal breeding needs is to identify and make use of them.

CONCLUSION

The statistical perspective, in the form of genomic selection, is the more applicable in contemporary breeding. Animal genomics researchers using from the sequence perspective are still working towards this the isolation of causative variants, equipped with new technologies but continuing a decades-long line of research.

New historical and philosophical perspectives on quantitative genetics

The aim of this virtual special issue is to bring together philosophical and historical perspectives to address long-standing issues in the interpretation, utility, and impacts of quantitative genetics methods and findings. Methodological approaches and the underlying scientific understanding of genetics and heredity have transformed since the field's inception. These advances have brought with them new philosophical issues regarding the interpretation and understanding of quantitative genetic results. The contributions in this issue demonstrate that there is still work to be done integrating old and new methodological and conceptual frameworks. In some cases, new results are interpreted using assumptions based on old concepts and methodologies that need to be explicitly recognised and updated. In other cases, new philosophical tools can be employed to synthesise historical quantitative genetics work with modern methodologies and findings. This introductory article surveys three general themes that have dominated philosophical discussion of quantitative genetics throughout history: (1) how methodologies have changed and transformed our knowledge and interpretations; (2) whether or not quantitative genetics can offer explanations relating to causation and prediction; and (3) the importance of defining the phenotypes under study. We situate the contributions in this virtual special issue within a historical framework addressing these three themes.

Simulated drought stress unravels differential response and different mechanisms of drought tolerance in newly developed tropical field corn inbreds

Corn is one of the most important cereal crops in the world with highest yield potential. Nevertheless, its potential productivity is constrained by the occurrences of drought stress worldwide. Besides, in the era of climate change, frequent occurrences of severe droughts are predicted. The present investigation was carried out at Main Agricultural Research Station, University of Agricultural Sciences, Dharwad in split plot design to study response of twenty-eight new corn inbreds under drought free (well-watered) conditions and drought simulated by withholding irrigation from 40 to 75 DAS to create water stress. Significant differences among the corn inbreds, moisture treatments and interaction between inbreds were observed for morpho-physiological, yield and yield components indicating differential response of corn inbreds. The inbreds CAL 1426-2 (higher RWC, SLW& wax and lower ASI), PDM 4641(higher SLW, proline, & wax, and lower ASI) and GPM 114 (higher proline & wax, and lower ASI) were drought tolerant. These inbreds are having higher production potential (>5.0 t/ha) under moisture stress condition with less per cent reduction (<24.4%) over non-moisture stress condition and hence are putative candidates for developing drought tolerant hybrids suitable for rainfed ecosystem besides using them in population improvement program to combine different drought tolerant mechanisms to evolve highly potent drought tolerant inbreds. The results of the study suggested that proline content, wax content, anthesis silking interval, relative water content can be better surrogate traits to identify drought tolerant inbreds in corn.

Evaluating indirect genetic effects of siblings using singletons

Estimating effects of parental and sibling genotypes (indirect genetic effects) can provide insight into how the family environment influences phenotypic variation. There is growing molecular genetic evidence for effects of parental phenotypes on their offspring (e.g. parental educational attainment), but the extent to which siblings affect each other is currently unclear. Here we used data from samples of unrelated individuals, without (singletons) and with biological full-siblings (non-singletons), to investigate and estimate sibling effects. Indirect genetic effects of siblings increase (or decrease) the covariance between genetic variation and a phenotype. It follows that differences in genetic association estimates between singletons and non-singletons could indicate indirect genetic effects of siblings if there is no heterogeneity in other sources of genetic association between singletons and non-singletons. We used UK Biobank data to estimate polygenic score (PGS) associations for height, BMI and educational attainment in self-reported singletons (N = 50,143) and non-singletons (N = 328,549). The educational attainment PGS association estimate was 12% larger (95% C.I. 3%, 21%) in the non-singleton sample than in the singleton sample, but the height and BMI PGS associations were consistent. Birth order data suggested that the difference in educational attainment PGS associations was driven by individuals with older siblings rather than firstborns. The relationship between number of siblings and educational attainment PGS associations was non-linear; PGS associations were 24% smaller in individuals with 6 or more siblings compared to the rest of the sample (95% C.I. 11%, 38%). We estimate that a 1 SD increase in sibling educational attainment PGS corresponds to a 0.025 year increase in the index individual's years in schooling (95% C.I. 0.013, 0.036). Our results suggest that older siblings may influence the educational attainment of younger siblings, adding to the growing evidence that effects of the environment on phenotypic variation partially reflect social effects of germline genetic variation in relatives.

Marker-assisted introgression of genes into rye translocation leads to the improvement in bread making quality of wheat (Triticum aestivum L.)

Introgression of genes from related species can be a powerful way to genetically improve crop yields, but selection for one trait can come at the cost to others. Wheat varieties with translocation of the short arm of chromosome 1 from the B genome of wheat (1BS) with the short arm of chromosome 1 from rye (1RS) are popular globally for their positive effect on yield and stress resistance. Unfortunately, this translocation (1BL.1RS) is also associated with poor bread making quality, mainly due to the presence of Sec-1 on its proximal end, encoding secalin proteins, and the absence of Glu-B3/Gli-B1-linked loci on its distal end, encoding low molecular weight glutenin subunits (LMW-GS). The present study aims to replace these two important loci on the 1RS arm with the wheat 1BS loci, in two popular Indian wheat varieties, PBW550 and DBW17, to improve their bread-making quality. Two donor lines in the cultivar Pavon background with absence of the Sec-1 locus and presence of the Glu-B3/Gli-B1 locus, respectively, were crossed and backcrossed with these two selected wheat varieties. In the advancing generations, marker assisted foreground selection was done for Sec-1^- and Glu-B3/Gli-B1⁺ loci while recurrent parent recovery was done with the help of SSR markers. BC₂F₅ and BC₂F₆ near isosgenic lines (NILs) with absence of Sec-1 and presence of Glu-B3/Gli-B1 loci were evaluated for two years in replicated yield trials. As a result of this selection, thirty promising lines were generated that demonstrated improved bread making quality but also balanced with improved yield-related traits compared to the parental strains. The study demonstrates the benefits of using marker-assisted selection to replace a few loci with negative effects within larger alien translocations for crop improvement.

An overview of international genetic evaluations of show jumping in sport horses

The breeding of sport horses to compete in the Olympic disciplines of show jumping, eventing, and dressage is fast becoming a global industry with the increased use of reproductive technologies, including artificial insemination and embryo transfer. Reproductive technologies have facilitated the dissemination of genetics from elite horses across multiple countries and breeds as breeders are no longer limited by location. Due to this increased level of crossbreeding, there is an increased need for estimated breeding values (EBVs) for sport horse performance that can be compared across breeds and countries. However, the implementation of across-breed or across-country genetic evaluations has been limited by the differences in each studbook’s individual breeding programs and genetic evaluations. Consequently, the aim of this review was to compare the genetic evaluations for show jumping of sport horse studbooks worldwide. The top sport horse studbooks in the world according to the World Breeding Federation for Sport Horses Studbook Rankings 2019 were contacted by email to request information on their current breeding programs and genetic evaluations. Twenty-six of the 51 studbooks contacted replied to this request but only 18 of these studbooks conducted their own genetic evaluations or were part of a larger genetic evaluation in their country of origin. The other eight studbooks were not involved in genetic evaluations at present but expressed an interest in the implementation of such in the future. Overall, many differences were identified among the genetic evaluations of each studbook or each country. The definition of show jumping performance differed within each evaluation and the methods and models utilized also differed. Despite some stallions and mares being registered in multiple studbooks or having progeny in multiple studbooks, these differences make comparison of EBVs across studbooks difficult. Further transparency and collaboration of sport horse studbooks with organizations such as Interstallion, will be essential to facilitate any future implementation of international genetic evaluations for show jumping performance.

Estimating FST and kinship for arbitrary population structures

F_ST and kinship are key parameters often estimated in modern population genetics studies in order to quantitatively characterize structure and relatedness. Kinship matrices have also become a fundamental quantity used in genome-wide association studies and heritability estimation. The most frequently-used estimators of F_ST and kinship are method-of-moments estimators whose accuracies depend strongly on the existence of simple underlying forms of structure, such as the independent subpopulations model of non-overlapping, independently evolving subpopulations. However, modern data sets have revealed that these simple models of structure likely do not hold in many populations, including humans. In this work, we analyze the behavior of these estimators in the presence of arbitrarily-complex population structures, which results in an improved estimation framework specifically designed for arbitrary population structures. After generalizing the definition of F_ST to arbitrary population structures and establishing a framework for assessing bias and consistency of genome-wide estimators, we calculate the accuracy of existing F_ST and kinship estimators under arbitrary population structures, characterizing biases and estimation challenges unobserved under their originally-assumed models of structure. We then present our new approach, which consistently estimates kinship and F_ST when the minimum kinship value in the dataset is estimated consistently. We illustrate our results using simulated genotypes from an admixture model, constructing a one-dimensional geographic scenario that departs nontrivially from the independent subpopulations model. Our simulations reveal the potential for severe biases in estimates of existing approaches that are overcome by our new framework. This work may significantly improve future analyses that rely on accurate kinship and F_ST estimates.

Kinship coefficients and F_ST, which measure relatedness and population structure, respectively, are important quantities needed to accurately perform various analyses on genetic data, including genome-wide association studies and heritability estimation. However, existing estimators require restrictive assumptions of independence that are not met by real human and other datasets. In this work we find that existing estimators can be severely biased under reasonable scenarios, first by theoretically determining their properties, and then using an admixture simulation to illustrate our findings. In particular, we find that existing F_ST estimators are downwardly biased, and that existing kinship matrix estimators have related biases that are on average downward and of similar magnitude but vary for every pair of individuals. These insights led us to a new estimation framework for kinship and F_ST that is practically unbiased for any population structure, as demonstrated by theory and simulations. Our new approaches—available as open-source R packages—are easy to use and are more widely applicable than existing approaches, and they are likely to improve downstream analyses that require accurate kinship and F_ST estimates.

Evaluation of variability and environmental stability of grain quality and agronomic parameters of pigmented rice (O. sativa L.)

Eleven pigmented rice genotypes were evaluated to estimate genetic parameters, heritability and association. The results indicated that, genotypic variation was high among the lines. The distinct seasonal effect on plant performance for antioxidant capacity, anthocyanin, flavonoids, head rice recovery and test weights was also observed. Wet season favoured the crop performance in all genotypes as compared to drought conditions. The differential accumulation of different quality traits such as AOA, anthocyanin content, flavonoids content, etc showed high heritability, which would be transfer to high yeilding popular rice cultivars through conventional or geneticaly modification techniques. The line Mamihunger was chosen as donor of the high-quality rice grain and Annapurna for high yield. Further, Mamihunger are foreseen to be good in nutritional quality and industry use.

Differential Masking of Natural Genetic Variation by miR-9a in Drosophila

Genetic variation is prevalent among individuals of the same species and yet the potential effects of genetic variation on developmental outcomes are frequently suppressed. Understanding the mechanisms that are responsible for this suppression is an important goal. Previously, we found that the microRNA miR-9a mitigates the impact of natural genetic variants that promote the development of scutellar bristles in adult Drosophila. Here we find that miR-9a does not affect the impact of genetic variants that inhibit the development of scutellar bristles. We show this using both directional and stabilizing selection in the laboratory. This specificity of action suggests that miR-9a does not interact with all functional classes of developmental genetic variants affecting sensory organ development. We also investigate the impact of miR-9a on a fitness trait, which is adult viability. At elevated physiological temperatures, miR-9a contributes to viability through masking genetic variants that hinder adult viability. We conclude that miR-9a activity in different developmental networks contributes to suppression of natural variants from perturbing development.

The 'missing heritability' of common disorders: should health researchers care?

This article critiques the "missing heritability" position, which calls for greater efforts and funding to identify the genetic architecture of common disorders, even if this endeavor has yet to translate into tangible prevention, diagnosis, or treatment interventions. Supporters of the position contend that genetic variants "for" common disorders, which they argue must exist based on heritability estimates (hence their "missing heritability" position), have not been found because the current state of science and technology is not adequate to the task, yet they insist that this search warrants significant societal investments. We argue, instead, that these variants have not been found because they do not exist. The thrust of the problem with the "missing heritability" position, we propose, lies in its proponents' use of faulty concepts and research methods, including reliance on twin studies, plagued with environmental confounds; on the concept of heritability, a breeding statistic and not a measure of the importance of genetic influences on phenotypes; and on the belief that genetic variations are relevant to understanding, preventing, or treating common disorders, a belief that we argue is false. We elaborate on these problems, discuss their public health implications, and suggest future directions for a critical analysis of human genetics.

Genetic architecture, inter-relationship and selection criteria for yield improvement in rice (Oryza sativa L.)

This study has been conducted to determine the extent of genetic association between yield of Rice (Oryza sativa L.) and its components. The present experiment was carried out with 40 Rice (Oryza sativa L.) genotypes which were evaluated in a randomized block design with 3 replications during wet season of 2007 and 2008. Results showed that sufficient amount of variability was found in the entire gene pool for all traits studied. Higher magnitude of genotypic and phenotypic coefficients of variation was recorded for seed yield, harvest index, biological yield, number of spikelets per panicle, flag leaf length, plant height and number of tillers indicates that these characters are least influence by environment. High heritability coupled with high genetic advance as percent of mean was registered for seed yield, harvest index, number of spikelets per panicle, biological yield and flag leaf length, suggesting preponderance of additive gene action in the expression of these characters. Grain yield was significantly and positively associated with harvest index, number of tillers per hill, number of panicle per plant, panicle length, number of spikelet's per panicle and test weight at both genotypic and phenotypic levels. Path coefficient analysis revealed that harvest index, biological yield, number of tillers per hill, panicle length, number of spikelets per panicle, plant height and test weight had direct positive effect on seed yield, indicating these are the main contributors to yield. From this study it may be concluded that harvest index, number of tillers per hill, panicle length and number of spikelet per panicle and test weight are the most important characters that contributed directly to yield. Thus, these characters may serve selection criteria for improving genetic potential of rice.

Quantitative genetic studies at the tetraploid and hexaploid levels in alfalfa

Two sets of diallel crosses involving seven tetraploid and five hexaploid alfalfa lines, previously selected for seed and forage yield, are studied. On the basis of combining ability and heritability estimates the following conclusion is drawn. The dominant and epistatic interactions (heterozygosity) are the major components in the expression of variability for yield and characters associated with yield in tetraploid populations. In hexaploid populations, however, there is an appreciable amount of additive variance, and the additive effect of genes along with interaction of various forms may account for the expressed variability for all the characters studied. Better genes and desirable interactions (possibly through heterozygosity) are the two essential genetic components of yield. The selection of better genes is feasible, but by itself will not produce the desired results. Future improvement may therefore depend on the utilization of heterosis and other forms of interactions. There is, in general, a very strong genetic correlation between yield and its components, and therefore, when a direct selection for yield is not feasible, the selection program may rely on a number of closely related characters.

Partitioning of variance and estimation of genetic parameters for various bristle number characters ofDrosophila melanogaster

Phenotypic variance for each of several bristle number characters (abdominal, sternopleural, second and third coxal) was partitioned using both hierarchal and dialled designs. Heritabilities and genetic correlations were estimated from parent-offspring regressions and correlations and half-sib correlations.A high proportion of the genetic variance for abdominal bristle number was due to epistatic and sex-linked gene action, but most of the genetic variance for the other characters was additive autosomal.The genetic correlations among sternopleural, and second and third coxal bristle numbers were all high, but that between abdominals and sternopleurals was low, while those between abdominals and either second or third coxals were virtually zero. An appreciable proportion of the covariance between abdominal and sternopleural bristle numbers was non-additive genetic.The diallel method gave more reliable estimates of genetic parameters when non-additive or sex-linked genetic variation was present.