Estimation of additive and non-additive genetic effects for fertility and reproduction traits in North American Holstein cattle using genomic information

Non-additive genetic effects are usually ignored in animal breeding programs due to data structure (e.g., incomplete pedigree), computational limitations and over-parameterization of the models. However, non-additive genetic effects may play an important role in the expression of complex traits in livestock species, such as fertility and reproduction traits. In this study, components of genetic variance for additive and non-additive genetic effects were estimated for a variety of fertility and reproduction traits in Holstein cattle using pedigree and genomic relationship matrices. Four linear models were used: (a) an additive genetic model; (b) a model including both additive and epistatic (additive by additive) genetic effects; (c) a model including both additive and dominance effects; and (d) a full model including additive, epistatic and dominance genetic effects. Nine fertility and reproduction traits were analysed, and models were run separately for heifers (N = 5,825) and cows (N = 6,090). For some traits, a larger proportion of phenotypic variance was explained by non-additive genetic effects compared with additive effects, indicating that epistasis, dominance or a combination thereof is of great importance. Epistatic genetic effects contributed more to the total phenotypic variance than dominance genetic effects. Although these models varied considerably in the partitioning of the components of genetic variance, the models including a non-additive genetic effect did not show a clear advantage over the additive model based on the Akaike information criterion. The partitioning of variance components resulted in a re-ranking of cows based solely on the cows’ additive genetic effects between models, indicating that adjusting for non-additive genetic effects could affect selection decisions made in dairy cattle breeding programs. These results suggest that non-additive genetic effects play an important role in some fertility and reproduction traits in Holstein cattle.     

稻米粒形和垩白度的QTL定位和上位性分析

 利用由181个家系组成的Lemont/特青籼粳交重组自交系群体,以及由161个RFLP、SSR标记和3个形态标记构建的全长为1916.5 cM、覆盖水稻基因组12 条染色体的连锁图,采用线性模型的复合区间作图方法（QTLMapper V10）,对粒长、粒宽、长宽比和垩白度等4个稻米品质性状的数量性状座位（QTL）进行了分析。在水稻的所有12 条染色体上共定位到7个加性主效QTL和19对上位性QTL,其中控制粒长、粒宽、长宽比的主效QTL各2个,控制垩白度的QTL 1个,分别解释12.8%、40.0%、26.0%和42.1%的表型变异;共检测到6对影响垩白度、6对影响粒长、7对影响长宽比的上位性QTL,分别解释52.2%、31.3%和38.2% 的表型变异。结果表明,上位性QTL和主效QTL一样在稻米粒形和垩白度的遗传中起着重要的作用。     

上位性及其对家养动物复杂经济性状形成的遗传学影响

Bateson于1909年最早将上位性(Epistasis)这个概念引入遗传学领域,在1918年,Fisher将不同位点上的非等位基因相互作用定义为上位性,非等位基因间的交互作用而产生的基因效应定位为上位效应(Epistaticeffect)。自此,在相当长的时期内,受到试验方法及技术手段的限制,研究者多采用以数量遗传学为主的研究方法对上位性开展研究。近年来,伴随着分子数量遗传学与功能基因组学的飞速发展,人们现在已获得大量的理论和实验证据支持上位效应对家养动物复杂性状的表型塑造以及复杂遗传系统演化机制存在重要的遗传学影响。文章拟对目前使用较为广泛的上位性概念、类型及主要的学术观点加以评述,着重介绍了这些概念的产生的背景、原理以及差别之处,并对上位性对家养动物复杂经济性状的遗传学影响给予简要介绍,以期能够为相关领域的研究者提供参考。     

Inheritance of Striga hermonthica adaptive traits in an early‐maturing white maize inbred line containing resistance genes from Zea diploperennis

Striga hermonthica can cause as high as 100% yield loss in maize depending on soil fertility level, type of genotype, severity of infestation and climatic conditions. Understanding the mode of inheritance of Striga resistance in maize is crucial for introgression of resistance genes into tropical germplasm and deployment of resistant varieties. This study examined the mode of inheritance of resistance to Striga in early‐maturing inbred line, TZdEI 352 containing resistance genes from Zea diploperennis. Six generations, P₁, P₂, F₁, F₂, BC₁P₁ and BC₁P₂ derived from a cross between resistant line, TZdEI 352 and susceptible line, TZdEI 425 were screened under artificial Striga infestation at Mokwa and Abuja, Nigeria, 2015. Additive‐dominance model was adequate in describing observed variations in the number of emerged Striga plants among the population; hence, digenic epistatic model was adopted for Striga damage. Dominance effects were higher than the additive effects for the number of emerged Striga plants at both locations signifying that non‐additive gene action conditioned inheritance of Striga resistance. Inbred TZdEI 352 could serve as invaluable parent for hybrid development in Striga endemic agro‐ecologies of sub‐Saharan Africa.     

水稻粒重及其相关性状的遗传解析

 应用292个 Lemont/ 特青F13重组自交系(RILs)和272个标记的遗传连锁图谱分析粒重及籽粒长、宽、厚、长/宽、体积和容重6个相关性状的遗传。所有性状在RILs中出现超亲分离。粒重与其他籽粒性状均呈显著正相关，而涉及籽粒品质的容重与粒宽、粒厚呈显著负相关。检测到影响粒重及其相关性状的主效QTL 48个和互作位点38对，这些QTL解释了各性状55%以上的表型变异。80%以上的主效QTL呈现一因多效或生理相关。QGl3和 QGl2等通过籽粒体积间接影响粒重， Lemont增效等位基因有利于籽粒品质的改良，而QGw5、QGt1和QGv7的特青增效等位基因增加粒重同时降低籽粒容重及品质。通过标记辅助选择进行不同QTL的重组，有望在增加粒重的同时改善籽粒品质。     

水稻显性核不育及其恢复性的遗传规律研究

 对萍乡显性核不育水稻的遗传规律进行了研究,结果表明该不育材料的育性是由两对显性核基因Ms和Rf互作控制的。其中Ms是显性不育基因,Rf是显性上位基因。两者共同存在时,显性上位基因能抑制显性不育基因的表达,从而使育性表现可育。其不育群体的遗传组成为Msmsrfrf+msmsrfrf或MsMsrfrf+MsMsRfRf,恢复系基因型为msmsRfRf。     

水稻耐热性的QTL定位及耐热性与光合速率的相关性

应用典型的籼粳交组合IR64×Azucena花药培养的DH群体及其已构建的分子连锁图谱,在田间及温室高温条件下对该DH群体的结实性状进行考查,采用QTLmapper 1.0软件检测控制结实率的加性和上位性效应的QTL。在第1、3、4、8和11等5条染色体上,共检测到6个具有加性效应的QTL,其中位于第1、3染色体的2个加性效应QTL来自父本Azucena的等位基因,它们是耐热的QTL,能分别提高结实率9.50和6.46个百分点,其贡献率分别为19.15%和2.86%;位于其余3条染色体的4个加性效应的QTL来自母本IR64的等位基因,它能提高结实率4.33~10.37个百分点,在第1、2、3、4、5、7、8、11等8条染色体之间还检测到8对加性×加性上位性效应,其贡献率为2.27%~8.13%。同时还对水稻分蘖盛期和抽穗期进行了光合速率的测定,发现抽穗期剑叶光合速率与耐热性呈显著的正相关。     

QTL Detection and Epistasis Analysis for Heading Date Using Single Segment Substitution Lines in Rice （Oryza sativa L.）

Heading date of rice is a key agronomic trait determining cultivated areas and seasons and affecting yield. In the present study, ifve primary single segment substitution lines with the same genetic background were used to detect quantitative trait loci （QTLs） for heading date in rice. Two QTLs, qHD3 and qHD6 on the short arm of chromosome 3 and the short arm of chromosome 6, respectively, were identiifed under natural long-day （NLD）. Nineteen secondary single segment substitution lines （SSSLs） and seven double segments pyramiding lines were designed to map the two QTLs and to evaluate their epistatic interaction between them. By overlapping mapping, qHD3 was mapped in a 791-kb interval between SSR markers RM3894 and RM569 and qHD6 in a 1 125-kb interval between RM587 and RM225. Results revealed the existence of epistatic interaction between qHD3 and qHD6 under natural long-day （NLD）. It was also found that qHD3 and qHD6 had signiifcant effects on plant height and yield traits, indicating that both of the QTLs have pleiotropic effects.     

Epistasis in the resistance of pepper to phytophthora stem blight (Phytophthora capsici L.) and its significance in the prediction of double cross performances

Summary Epistatic effects are present in the resistance to Phytophthora capsici in peppers (Capsicum annuum). Genetic statistical analysis shows that additive by additive epistasis as well as higher order epistatic effects contribute to the total variation of resistance, significantly. Higher order epistatic effects caused bias in the prediction of the performance of double crosses, the difference between observed and predicted performances being significant.The relative importance of higher order epistasis with respect to additive by additive epistasis seems to be correlated with the aggressiveness of the isolate of Phytophthora capsici.     

Genetics of spike length in durum wheat

Gene effects were analyzed using mean spike length of 12 populations, viz., both parents, F₁, F₂, first back cross generation, BC₁ and BC₂, second backcross generations, BC₁₁,BC₁₂, BC₂₁ and BC₂₂ along with BC₁ self and BC₂ self derived by selfing BC₁ and BC₂populations of three crosses involving six diverse cultivars of Triticum durumto determine the nature of gene actions governing spike length through generation mean analysis under normal and late sown environments. The six-parameter model was adequate in most of the cases to explain genetic variation among the generation means under both the sowing environments. Additive (d) gene effect was significant in all the cases, whereas dominance (h) gene effect was not so frequently observed significant. Epistatic effects, particularly digenic types were predominant over additive and dominance effects in most of the cases under both normal and late sown environments except in the cross Cocorit 71 × A-9-30-1 (normal sown).Additive × dominance × dominance (y), trigenic interaction played significant role in controlling the inheritance of this trait in the cross HI 8062 × JNK-4W-128under late sown condition. Duplicate epistasis was observed in the cross HI 8062× JNK-4W-128 (normal sown). Non-fixable gene effects were of higher magnitude than fixable gene effects in almost all cases, confirmed the major role of non-additive gene effects to control the inheritance of spike length in durum wheat. Significant heterosis over better parent was not observed. Similarly, inbreeding depression was not commonly observed. Favourable and suitable environment must be considered before finalizing breeding programme for its simple inheritance to get desirable improvement for high grain yield. Hybridization systems, such as biparental mating and / or diallel selective mating, which exploit both additive and non-additive gene effects, simultaneously, could be useful in the improvement of spike length in durum wheat. This revised version was published online in July 2006 with corrections to the Cover Date.