A Genetic Basis Behind Combining Ability and Breeding Values in Mono- and Di-genic Systems

Combining ability and breeding values are concepts of crucial importance in practical breeding. However, in early literature, methods of partitioning the genetic value into additive and dominance effects were described mostly in single gene and under random mating. Though average effect and average excess of gene substitution were defined by Fisher and a practial method of obtaining breeding values outlined by Falconer, concerted attempts are scarce in integrating the concepts of combining ability, breeding value and additive effects. Only a few workers have reported the values of those parameters for inbred populations while published reports on those effects in digenic systems with linkage appear to be not readily available. Practical breeders continue to use those concepts as if they were independent. This paper is therefore an attempt at filling the research gaps and setting those concepts in proper practical perspective.     

Genetic quality and sexual selection: an integrated framework for good genes and compatible genes

Why are females so choosy when it comes to mating? This question has puzzled and marveled evolutionary and behavioral ecologists for decades. In mating systems in which males provide direct benefits to the female or her offspring, such as food or shelter, the answer seems straightforward — females should prefer to mate with males that are able to provide more resources. The answer is less clear in other mating systems in which males provide no resources (other than sperm) to females. Theoretical models that account for the evolution of mate choice in such nonresource-based mating systems require that females obtain a genetic benefit through increased offspring fitness from their choice. Empirical studies of nonresource-based mating systems that are characterized by strong female choice for males with elaborate sexual traits (like the large tail of peacocks) suggest that additive genetic benefits can explain only a small percentage of the variation in fitness. Other research on genetic benefits has examined nonadditive effects as another source of genetic variation in fitness and a potential benefit to female mate choice. In this paper, we review the sexual selection literature on genetic quality to address five objectives. First, we attempt to provide an integrated framework for discussing genetic quality. We propose that the term ‘good gene’ be used exclusively to refer to additive genetic variation in fitness, ‘compatible gene’ be used to refer to nonadditive genetic variation in fitness, and ‘genetic quality’ be defined as the sum of the two effects. Second, we review empirical approaches used to calculate the effect size of genetic quality and discuss these approaches in the context of measuring benefits from good genes, compatible genes and both types of genes. Third, we discuss biological mechanisms for acquiring and promoting offspring genetic quality and categorize these into three stages during breeding: (i) precopulatory (mate choice); (ii) postcopulatory, prefertilization (sperm utilization); and (iii) postcopulatory, postfertilization (differential investment). Fourth, we present a verbal model of the effect of good genes sexual selection and compatible genes sexual selection on population genetic variation in fitness, and discuss the potential trade-offs that might exist between mate choice for good genes and mate choice for compatible genes. Fifth, we discuss some future directions for research on genetic quality and sexual selection.     

Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection

We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stochastic simulation and compared the mating criteria in hierarchical and factorial breeding schemes, where the animals were selected based on breeding values predicted by animal-model BLUP. Random mating was included as a reference-mating criterion. We found that MCAC mating generated 4% to 8% less inbreeding than minimum-coancestry mating in the hierarchical and factorial breeding schemes without any loss in genetic gain. Moreover, it generated upto 28% less inbreeding and about 3% more genetic gain than random mating. The benefits of MCAC mating over minimum-coancestry mating are worthwhile because they can be achieved without extra costs or practical constraints. MCAC mating merely uses pedigree information to pair the animals more appropriately and is clearly a worthy alternative to minimum-coancestry mating and probably any other mating criterion. We believe, therefore, that MCAC mating should be used in breeding schemes where pedigree information is available.     

多性状综合遗传效应测定方法的研究

应用主成分分析原理提出测定多个交配组合多性状综合遗传效应的方法,将多性状综合遗传效 各主成分遗传效应与其相对重要树重乘积和,此法消除了性状间相关和环境因素的影响,得到的多性状综合遗传效应可以互相比较,便于选出最佳交配组合用于动物生产。     

Direct and indirect assortative mating: a multivariate approach to plant flowering schedules

This paper develops methods to partition the phenotypic correlation between mates for a focal trait--the standard measure for assortative mating--into a direct component and additional indirect components. Indirect assortative mating occurs when a nonassorting trait is correlated within individuals to a directly assorting trait. Direct and indirect assortative mating is assessed for flowering phenology in Brassica rapa. The flowering time of pollen recipients (mothers) was strongly correlated (rho=0.67) to that of potential pollen donors (fathers). Similarly, recipients and donors were correlated for duration of their flowering periods (rho=0.32) and stem diameters (rho=0.52). A partitioning of between-mate correlations revealed direct assortative mating for flowering time and period duration. However, assortment for stem diameter is explained solely through its correlation to flowering time. Examination of standard quantitative genetic theory shows that indirect assortative mating inflates genetic variance in a focal trait and the genetic covariance between focal and phenotypically correlated traits.     

Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems

Both mating system and population history can have large impacts on genetic diversity and population structure. Here, we use multilocus sequence data to investigate how these factors impact two closely related Brassicaceae species: the selfing Capsella rubella and the outcrossing C. grandiflora. To do this, we have sequenced 16 loci in approximately 70 individuals from 7 populations of each species. Patterns of population structure differ strongly between the two species. In C. grandiflora, we observe an isolation-by-distance pattern and identify three clearly delineated genetic groups. In C. rubella, where we estimate the selfing rate to be 0.90-0.94, the pattern is less clear with some sampling populations forming separate genetic clusters while others are highly mixed. The two species also have divergent histories. Our analysis gives support for a bottleneck approximately 73 kya (20-139 kya) in C. rubella, which most likely represents speciation from C. grandiflora. In C. grandiflora, there is moderate support for the standard neutral model in 2 of 3 genetic clusters, while the third cluster and the total data set show evidence of expansion. It is clear that mating system has an impact on these two species, for example affecting the level of genetic variation and the genetic structure. However, our results also clearly show that a combination of past and present processes, some of which are not affected by mating system, is needed to explain the differences between C. rubella and C. grandiflora.     

鹅掌楸不同交配组合子代遗传多样性分析

揭示不同交配类型与子代遗传多样性的关系, 对于林木杂交育种及种子园管理具有理论与实践意义。文章选取来自鹅掌楸、北美鹅掌楸及杂交鹅掌楸的16个交配亲本, 共组配14个杂交组合, 分属5种交配类型, 分别为种间杂交、种内交配、多父本混合授粉、回交、以及自交。每个交配组合随机抽取30个子代, 利用SSR分子标记检测各子代群体遗传多样性以及16个交配亲本间的遗传距离。结果表明, 总体上, 鹅掌楸交配子代群体具有较高的遗传多样性。5种交配类型子代群体中, 遗传多样性水平由高至低的趋势为: 多父本混合授粉子代、种间交配子代、杂种F1与亲本的回交子代、种内交配子代, 自交子代。子代遗传多样性与亲本间遗传距离呈显著正相关, 表明亲本间遗传距离大, 则子代遗传多样性高。相同亲本正反交子代群体的遗传多样性差别不明显。     

OUTBREEDING DEPRESSION WITH LOW GENETIC VARIATION IN SELFING CAENORHABDITIS NEMATODES

Theory and empirical study produce clear links between mating system evolution and inbreeding depression. The connections between mating systems and outbreeding depression, whereby fitness is reduced in crosses of less related individuals, however, are less well defined. Here we investigate inbreeding and outbreeding depression in self‐fertile androdioecious nematodes, focusing on Caenorhabditis sp. 11. We quantify nucleotide polymorphism for nine nuclear loci for strains throughout its tropical range, and find some evidence of genetic differentiation despite the lowest sequence diversity observed in this genus. Controlled crosses between strains from geographically separated regions show strong outbreeding depression, with reproductive output of F1s reduced by 36% on average. Outbreeding depression is therefore common in self‐fertilizing Caenorhabditis species, each of which evolved androdioecious selfing hermaphroditism independently, but appears strongest in C. sp. 11. Moreover, the poor mating efficiency of androdioecious males extends to C. sp. 11. We propose that self‐fertilization is a key driver of outbreeding depression, but that it need not evolve as a direct result of local adaptation per se. Our verbal model of this process highlights the need for formal theory, and C. sp. 11 provides a convenient system for testing the genetic mechanisms that cause outbreeding depression, negative epistasis, and incipient speciation.     

Multiple paternity is related to adult sex ratio and sex determination system in reptiles

The adult sex ratio (ASR, the proportion of males in the adult population) is an emerging predictor of reproductive behaviour, and recent studies in birds and humans suggest it is a major driver of social mating systems and parental care. ASR may also influence genetic mating systems. For instance male-skewed ASRs are expected to increase the frequency of multiple paternity (defined here as a clutch or litter sired by two or more males) due to higher rates of coercive copulations by males, and/or due to females exploiting the opportunity of copulation with multiple males to increase genetic diversity of their offspring. Here, we evaluate this hypothesis in reptiles that often exhibit high frequency of multiple paternity although its ecological and life-history predictors have remained controversial. Using a comprehensive dataset of 81 species representing all four non-avian reptile orders, we show that increased frequency of multiple paternity is predicted by more male-skewed ASR, and this relationship is robust to simultaneous effects of several life-history predictors. Additionally, we show that the frequency of multiple paternity varies with the sex determination system: species with female heterogamety (ZZ/ZW sex chromosomes) exhibit higher levels of multiple paternity than species with male heterogamety (XY/XX) or temperature-dependent sex determination. Thus, our across-species comparative study provides the first evidence that genetic mating system depends on ASR in reptiles. We call for further investigations to uncover the complex evolutionary associations between mating systems, sex determination systems and ASR.     

Mating schemes for optimum contribution selection with constrained rates of inbreeding

The effect of non-random mating on genetic response was compared for populations with discrete generations. Mating followed a selection step where the average coancestry of selected animals was constrained, while genetic response was maximised. Minimum coancestry (MC), Minimum coancestry with a maximum of one offspring per mating pair (MC1) and Minimum variance of the relationships of offspring (MVRO) mating schemes resulted in a delay in inbreeding of about two generations compared with Random, Random factorial and Compensatory mating. In these breeding schemes where selection constrains the rate of inbreeding, ΔF, the improved family structure due to non-random mating increased genetic response. For schemes with ΔF constrained to 1.0% and 100 selection candidates, genetic response was 22% higher for the MC1 and MVRO schemes compared with Random mating schemes. For schemes with a less stringent constraint on ΔF or more selection candidates, the superiority of the MC1 and MVRO schemes was smaller (5–6%). In general, MC1 seemed to be the preferred mating method, since it almost always yielded the highest genetic response. MC1 mainly achieved these high genetic responses by avoiding extreme relationships among the offspring, i.e. fullsib offspring are avoided, and by making the contributions of ancestors to offspring more equal by mating least related animals.     

An analysis of genetic differentiation among assortatively mating Drosophila melanogaster in Zimbabwe

African Drosophila melanogaster populations, and those from Zimbabwe in particular, have attracted much interest recently. African flies differ genetically from 'cosmopolitan' populations and were found to exhibit discriminative mating behaviour against individuals from 'cosmopolitan' populations. It has therefore been proposed that Zimbabwean and some other African populations are in an 'incipient stage of speciation'. However, whether the mating behaviour is an effective barrier against gene flow from other populations, and whether intra-population genetic differentiation has already evolved in sympatry is not known. Here, we took a population-based approach to test whether the well-characterized mating type differences have resulted in a genome-wide differentiation at the population level. Using 122 polymorphic microsatellite loci mapping to the third chromosome, we demonstrate a significant genetic differentiation between Zimbabwean flies differing in their mating behaviour. We also provide evidence to suggest that this difference is unlikely to be attributable to population structure within Zimbabwe. However, the analysis of individual microsatellite loci did not indicate more loci differentiating these two groups than expected by chance. Our data suggest that the 'Z'-'M' mating behaviour is strong enough to result in a small but significant genetic differentiation. Thus, future studies based on a larger population sample of flies characterized for their mating behaviour and using more markers are expected to provide more information on the genetic basis of the mating traits in the Zimbabwe flies.     

中国马铃薯晚疫病菌AFLP遗传多样性分析

应用AFLP分子标记检测了我国部分马铃薯主要产区马铃薯晚疫病菌的遗传多样性及不同地区菌株间的亲缘关系。在200对引物组合中,利用6个菌株筛选出12对多态性好、带型清晰的引物组合。利用这12对引物组合对1997-2002年间采自我国黑龙江、河北、四川和云南4省的50株菌株进行了PCR扩增,共扩增出922条谱带,其中多态性标记530条,占57.5%。利用NTSYSpc软件中UPGMA算法构建了我国马铃薯晚疫病菌的亲缘关系树状图,聚类分析结果表明我国马铃薯晚疫病菌的遗传多样性与病原菌的地理来源有一定的相关性,而与交配型、生理小种和对甲霜灵的抗性无明显的相关性。用POPGENE软件计算了各群体间的遗传多样性参数,结果表明我国马铃薯晚疫病菌的遗传多样性程度不高,不同地区种群间分化不明显。     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei （Primulaceae）： implications for its conservation

Omphalogramma souliei Franch. is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. souliei in NW Yunnan, China. The genetic diversity at the species level is low with P=42.5% （percentage of polymorphic bands） and Hsp=0.1762 （total genetic diversity）. However, a high level of genetic differentiation among populations was detected based on different measures （Nei＇s genetic diversity analysis： Gst=0.6038; AMOVA analysis： Fst=0.6797）. Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenogamy predominated and autogamy played an assistant role in O. souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

Non-random mating for selection with restricted rates of inbreeding and overlapping generations

Minimum coancestry mating with a maximum of one offspring per mating pair (MC1) is compared with random mating schemes for populations with overlapping generations. Optimum contribution selection is used, whereby ΔF is restricted. For schemes with ΔF restricted to 0.25% per year, 256 animals born per year and heritability of 0.25, genetic gain increased with 18% compared with random mating. The effect of MC1 on genetic gain decreased for larger schemes and schemes with a less stringent restriction on inbreeding. Breeding schemes hardly changed when omitting the iteration on the generation interval to find an optimum distribution of parents over age-classes, which saves computer time, but inbreeding and genetic merit fluctuated more before the schemes had reached a steady-state. When bulls were progeny tested, these progeny tested bulls were selected instead of the young bulls, which led to increased generation intervals, increased selection intensity of bulls and increased genetic gain (35% compared to a scheme without progeny testing for random mating). The effect of MC1 decreased for schemes with progeny testing. MC1 mating increased genetic gain from 11–18% for overlapping and 1–4% for discrete generations, when comparing schemes with similar genetic gain and size.     

Stochastic modelling of shifts in allele frequencies reveals a strongly polygynous mating system in the re‐introduced Asiatic wild ass

Small populations are prone to loss of genetic variation and hence to a reduction in their evolutionary potential. Therefore, studying the mating system of small populations and its potential effects on genetic drift and genetic diversity is of high importance for their viability assessments. The traditional method for studying genetic mating systems is paternity analysis. Yet, as small populations are often rare and elusive, the genetic data required for paternity analysis are frequently unavailable. The endangered Asiatic wild ass (Equus hemionus), like all equids, displays a behaviourally polygynous mating system; however, the level of polygyny has never been measured genetically in wild equids. Combining noninvasive genetic data with stochastic modelling of shifts in allele frequencies, we developed an alternative approach to paternity analysis for studying the genetic mating system of the re‐introduced Asiatic wild ass in the Negev Desert, Israel. We compared the shifts in allele frequencies (as a measure of genetic drift) that have occurred in the wild ass population since re‐introduction onset to simulated scenarios under different proportions of mating males. We revealed a strongly polygynous mating system in which less than 25% of all males participate in the mating process each generation. This strongly polygynous mating system and its potential effect on the re‐introduced population's genetic diversity could have significant consequences for the long‐term persistence of the population in the Negev. The stochastic modelling approach and the use of allele‐frequency shifts can be further applied to systems that are affected by genetic drift and for which genetic data are limited.     

光核桃遗传资源的经济价值评估与保护

本文将光核桃遗传资源的经济价值划分为直接利用价值、间接利用价值和潜在利用价值,采用市场价格法、旅行费用法、防护费用法及类比分析法等方法对光核桃遗传资源的经济价值进行估算,并提出该资源保护与管理建议。光核桃遗传资源经济价值的评估,将为具有潜在巨大经济价值的生物遗传资源管理提供价值评估方法,同时为维护国家利益、制订生物多样性保护与管理政策及建立生物遗传资源惠益分享制度提供技术支持。     

Unbiased relatedness estimation in structured populations

Knowledge of the genetic relatedness between individuals is important in many research areas in quantitative genetics, conservation genetics, forensics, evolution, and ecology. In the absence of pedigree records, relatedness can be estimated from genetic marker data using a number of estimators. These estimators, however, make the critical assumption of a large random mating population without genetic structures. The assumption is frequently violated in the real world where geographic/social structures or nonrandom mating usually lead to genetic structures. In this study, I investigated two approaches to the estimation of relatedness between a pair of individuals from a subpopulation due to recent common ancestors (i.e., relatedness is defined and measured with the current focal subpopulation as reference). The indirect approach uses the allele frequencies of the entire population with and without accounting for the population structure, and the direct approach uses the allele frequencies of the current focal subpopulation. I found by simulations that currently widely applied relatedness estimators are upwardly biased under the indirect approach, but can be modified to become unbiased and more accurate by using Wright's F(st) to account for population structures. However, the modified unbiased estimators under the indirect approach are clearly inferior to the unmodified original estimators under the direct approach, even when small samples are used in estimating both allele frequencies and relatedness.     

植物的交配系统与濒危植物的保护繁育策略

植物的交配系统在理论上被视为影响种群遗传结构最为显著的因素之一。在具体实践中,指导着遗传育种和濒危植物的保护。本文首先剖析了交配系统及其相关的概念,并简要回顾交配系统研究的历史、重要的理论模型和方法。然后说明交配系统与种群遗传结构的具体关系,进而讨论交配系统在濒危植物进化与适应中的作用。最后说明交配系统的信息在就地与迁地保护中的重要性。     

Why do females mate multiply? A review of the genetic benefits

The aim of this review is to consider the potential benefits that females may gain from mating more than once in a single reproductive cycle. The relationship between non-genetic and genetic benefits is briefly explored. We suggest that multiple mating for purely non-genetic benefits is unlikely as it invariably leads to the possibility of genetic benefits as well. We begin by briefly reviewing the main models for genetic benefits to mate choice, and the supporting evidence that choice can increase offspring performance and the sexual attractiveness of sons. We then explain how multiple mating can elevate offspring fitness by increasing the number of potential sires that compete, when this occurs in conjunction with mechanisms of paternity biasing that function in copula or post-copulation. We begin by identifying cases where females use pre-copulatory cues to identify mates prior to remating. In the simplest case, females remate because they identify a superior mate and 'trade up' genetically. The main evidence for this process comes from extra-pair copulation in birds. Second, we note other cases where pre-copulatory cues may be less reliable and females mate with several males to promote post-copulatory mechanisms that bias paternity. Although a distinction is drawn between sperm competition and cryptic female choice, we point out that the genetic benefits to polyandry in terms of producing more viable or sexually attractive offspring do not depend on the exact mechanism that leads to biased paternity. Post-copulatory mechanisms of paternity biasing may: (1) reduce genetic incompatibility between male and female genetic contributions to offspring; (2) increase offspring viability if there is a positive correlation between traits favoured post-copulation and those that improve performance under natural selection; (3) increase the ability of sons to gain paternity when they mate with polyandrous females. A third possibility is that genetic diversity among offspring is directly favoured. This can be due to bet-hedging (due to mate assessment errors or temporal fluctuations in the environment), beneficial interactions between less related siblings or the opportunity to preferentially fertilise eggs with sperm of a specific genotype drawn from a range of stored sperm depending on prevailing environmental conditions. We use case studies from the social insects to provide some concrete examples of the role of genetic diversity among progeny in elevating fitness. We conclude that post-copulatory mechanisms provide a more reliable way of selecting a genetically compatible mate than pre-copulatory mate choice. Some of the best evidence for cryptic female choice by sperm selection is due to selection of more compatible sperm. Two future areas of research seem likely to be profitable. First, more experimental evidence is needed demonstrating that multiple mating increases offspring fitness via genetic gains. Second, the role of multiple mating in promoting assortative fertilization and increasing reproductive isolation between populations may help us to understand sympatric speciation.     

The Fundamental Theorem of Natural Selection in Ewens'' Sense (Case of Fertility Selection)

We show that the Fundamental Theorem of Natural Selection in Ewens' sense is valid in the case of fertility selection: the additive genetic variance in fertility divided by the mean fertility is exactly equal to the partial change in the mean fertility from the current generation to the next. This partial change is the increase in the mean additive value caused by frequency changes from one generation to the next but keeping unchanged the additive values. The only hypothesis on mating is that it does not affect the allelic frequencies in the sense that these are the same before and after mating in the parental generation, which occurs for a wide range of mating patterns going from random mating to several regular systems of inbreeding and cases of assortative mating. The fertility of couples is determined by the genes at an arbitrary number of loci, and the additive (average) allelic effects are defined by a linear system of equations, which is used to extend Ewens' optimality principle to the case of fertility selection.