Inbreeding and genetic load in a pair of sibling grouse species:Tetrastes sewersowi and T.bonasia

Genetic load and inbreeding are recognized as important factors to be considered in conservation programs.Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals,including humans(inbreeding depression).Genomic tech-niques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation.We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both.We found a large range of inbreeding measured as FROH(fraction of runs of homozygosity)in individuals from different populations of Chinese Grouse(Tetrastes sewerzowi)and Hazel Grouse(T.bonasia).FROH estimated from genome-wide runs of homozygosity(ROH)ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse.Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse(including samples from Sweden,Germany and Northeast Poland)were the most inbred(FROH ranged from 0.10 to 0.23 and 0.11 to 0.44,respectively).These levels are comparable to other highly inbred populations of birds.Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels.Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse.These results are possibly explained by higher fixation rates,mutational melt down,in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse.However,when we compared the relatively more severe class of loss-of-function muta-tions,Hazel Grouse had slightly higher levels than Chinese Grouse,a result which may indicate that purifying selection(purging)has been more efficient in Chinese Grouse on this class of mutations.

Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic animals.But after multi-generation selection,the rate of inbreeding and the occurrence of homozygous harmful alleles might increase,which would reduce performance and genetic diversity.To mitigate the above problems,we can utilize genomic mating(GM)based upon optimal mate allocation to construct the best genotypic combinations in the next generation.In this study,we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population.These factors included:the algorithm used to derive inbreeding coefficients;the trait heritability(0.1,0.3 or 0.5);the kind of GM scheme(focused average GEBV or inbreeding);the approach for computing the genomic relationship matrix(by SNP or runs of homozygosity(ROH)).The outcomes were compared to three traditional mating schemes(random,positive assortative or negative assortative matings).In addition,the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.Results Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain.The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs.The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6%higher rates of genetic gainΔG,and 13%-83.3%lowerΔF than positive assortative mating regardless of heritability.The rates of inbreeding were always the fastest with positive assortative mating.Results from a purebred Large White pig population,confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.Conclusion Compared with traditional mating schemes,genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population.Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.

Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book:the case of the Pura Raza Española horse

Background:Estimating inbreeding,which is omnipresent and inevitable in livestock populations,is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding.Inbreeding coefficients have been historically estimated by using pedigree information;however,over the last decade,genome-base inbreeding coefficients have come to the forefront in this field.The Pura Raza Espanola(PRE)horse is an autochthonous Spanish horse breed which has been recognised since 1912.The total PRE population(344,718 horses)was used to estimate Classical(F),Ballou’s ancestral,Kalinowski’s ancestral,Kalinowski’s new and the ancestral history coefficient values.In addition,genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques(methods of moments-FHOM-,the diagonal elements of the genomic-FG-,and hybrid matrixes-FH-)and ROH measures(FRZ).The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse,with proven parenteral information for the last 40 years and a high degree of completeness(over 90%for the last 70 years)will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.Results:The mean values of the pedigree-based inbreeding coefficients ranged from 0.01(F for the last 3 generations-F3-)to 0.44(ancestral history coefficient)and the mean values of genomic-based inbreeding coefficients varied from 0.05(FRZ for three generations,FH and FHOM)to 0.11(FRZ for nine generations).Significant correlations were also found between pedigree and genomic inbreeding values,which ranged between 0.58(F3 with FHOM)and 0.79(F with FRZ).In addition,the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values,and the opposite when ancient values are calculated.Conclusions:Ultimately,our results show that it is still useful to work with a deep and reliable pedigree in pedigreebased genetic studies with very large effective population sizes.Obtaining a satisfactory parameter will always be desirable,but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

东极黑猪群体遗传结构分析及利用

东极黑猪是在我国东北部发现的一种新黑猪群体,试验旨在了解东极黑猪群体结构和遗传多样性,以期更好地保护和利用东极黑猪遗传资源。通过50k SNP芯片研究426头东极黑猪进行遗传多样性、亲缘关系和家系结构,同时加入20头大白猪及20头民猪数据开展主成分分析(Principal component analysis,PCA)。结果表明,东极黑猪57466个SNPs中有47389个SNPs通过质检;PCA结果显示,3个群体分别聚类,东极黑猪与另外两个猪种区分明显;东极黑猪群体中部分个体遗传关系较近,状态同源(Identity by state,IBS)遗传距离为0.0977~0.3589,平均值为0.2752;连续性纯合片段(Runs of homozygosity,ROH)分析发现该群体平均ROH为317.3 Mb,主要分布在200~300 Mb,群体平均近交系数(FROH)为0.133,说明存在近交情况。根据基因组亲缘关系和聚类分析结果,可将东极黑猪群体分为15个家系。综合分析表明,东极黑猪群体遗传多样性丰富,品种独特,但存在近交,建议引入新血统以防遗传多样性丢失。

基于GBS测序的湘东黑山羊的亲缘关系及近交系数

利用基因分型测序(GBS)对60只湘东黑山羊(9只公羊、51只母羊)进行基因组测序,获得湘东黑山羊染色体上的SNP数据和连续纯合子片段(ROH)数据。通过SNP数据进行基于G矩阵的基因组亲缘关系分析和NJ聚类分析,构建湘东黑山羊的群体家系结构,并通过ROH数据得到群体平均近交系数。结果表明,60只湘东黑山羊的平均测序深度为9.15X,与参考基因组比对率平均为99.59%;在SNP检测过程中,3只母羊不符合基因型数据质控标准,将其过滤后获得其他57只黑山羊29条染色体上153046个SNPs位点和1937个ROH片段;构建的湘东黑山羊8个家系,其中9只公羊和6只母羊被分为7个家系,另42只母羊被单独分类;基于ROH片段分析的湘东黑山羊群体中每个个体的近交系数均值为0.047,说明湘东黑山羊公羊在繁育过程中有较大的利用空间。

观赏蕨类姬蕨同配子体自交的孢子体萌发和发育特性

[目的]评估交配形式对蕨类繁殖的影响。[方法]以姬蕨(Hypolepis punctata)为例,设计配子体单独培养(同配自交)和混合培养(混交)比较试验,比较两种交配系统下孢子体萌发状态(萌发率、存活率),孢子体成长情况及生长速率。[结果]尽管自交幼苗生长趋势弱于混交个体,单独培养产生的完全纯合的姬蕨孢子体最终存活率达到62.5%,说明蕨类的自交确实可以导致近交衰退,但仍然具有可接受的存活能力,单个孢子仍有很大概率上延续种群。蕨类植物由于其特殊的生活史特性,可通过单独培养得到完全纯合的自交个体,从而得到性状稳定的品系。[结论]该研究中单独培养技术在园艺育种方向具有很好的应用前景。

虾夷扇贝F_(1)自交衰退及其遗传调控机理

近交导致的种质退化严重影响虾夷扇贝养殖产业。为探明虾夷扇贝近交衰退的现象及遗传调控机理,在表型水平上,构建近交系数分别为0.5、0.25和0的自交组、近交组与自然群体对照组,追踪不同近交系数下虾夷扇贝幼虫期到成体期530日龄的性状差异,同时选取7个适合度性状,利用主成分分析法构建基于近交衰退的适合度指标评价方法;在基因组水平上,利用1个自交家系的亲本及其21个子代进行全基因组重测序,开展标记偏分离分析。试验结果显示:针对存活率性状,在幼虫期,自交组近交衰退率是近交组的1.31~3.05倍;在成体期,自交组近交衰退率是近交组的0.97~7.29倍。而生长性状,在幼虫期,仅有自交组保持较低的近交衰退率(1.65%~2.56%);在成体期,自交组与近交组几乎未发生衰退。基于重测序分型得到1253519个单核苷酸多态性用于偏分离统计,约99%在子代中发生了显著的偏分离,其中23%属于配子偏分离、77%属于合子偏分离,合子偏分离中有89%为杂合子过剩,即超显性效应起作用,仅10%受显性效应影响为纯合子缺失。试验结果表明,超显性效应及偏分离作用在虾夷扇贝F_(1)子代存活率性状的自交衰退中起主要作用,为近交衰退的机理提供更有力证据的同时,也为虾夷扇贝种质遗传改良提供了有效思路。

基因组选配研究及其在畜禽育种中的应用

基因组选配(genomic mating,GM)是利用基因组估计育种值、风险指数(有效性)、交配亲本互补信息等概念进行选配优化的方法,其侧重于最佳的交配组合而不是截断式选择,可以有效控制群体近交速率的增长、维持遗传多样性,是基因组时代下最具前瞻性的理论方法,具有更高的可行性、有效性,有望实现长期可持续的遗传进展。本文介绍了基因组选配的基本概念、原理与方法,并综述了畜禽育种中利用基因组信息优化选配的应用现状。此外,还提出了基因组选配亟待解决的问题以及未来研究方向。通过对这些问题的探索和研究,进一步提升基因组选配的效果,为推动畜禽育种的长期可持续发展提供参考。

利用“黄海芯1号”55K SNP芯片评估凡纳滨对虾选育群体的遗传多样性与基因组近交水平

凡纳滨对虾的主要选育目标分为两个方面:一是培育具有较强抗病、抗逆性的“高抗系”(GK),二是培育具有快速生长特性的“快大系”(KD)。然而,国内缺少针对这两个选育群体的遗传多样性特别是基因组近交水平的调查分析研究。基于液相芯片“黄海芯1号”(55 K SNP)的基因分型数据,首次分析了GK(1064尾个体)和KD(564尾个体)选育群体的遗传结构和遗传多样性,调查了连续性纯合片段(ROH)的基因组分布特征,并重点评估了两个群体的基因组近交水平。PCA及进化树分析表明GK及KD群体可明确分层,亲缘关系热图表明KD群体内个体间的亲缘关系比GK群体更近。GK群体包括的家系数量更多,导致其遗传多样性高于KD群体;两群体间的F_(st)为0.09,存在中等遗传分化。GK和KD群体每个ROH的平均长度分别为(1.70±0.34)Mb和(1.65±0.38)Mb,每个样本ROH的平均数量分别为1.98±1.30和2.07±1.37。GK和KD群体0.8~1.25 Mb长度的ROH占比分别为11.41%和19.17%,表明KD群体的选育历史比GK群体更长。两个群体>2.25 Mb长度的ROH片段占比分别为10.26和9.74%,表明两个群体短期内未发生近亲交配。七种基因组近交系数评估结果表明,KD群体的近交水平高于GK群体。不依赖基础群体等位基因频率的F_(ROH)和F_(HOM)方法可准确地评价育种群体的真实近交水平,而F_(VR1)、F_(YA1)和F_(LH1)等依赖基础群体等位基因频率的方法可以用来比较群体及个体间的相对近交水平。上述结果为准确地评估育种群体的近交水平和优化育种方案提供了重要参考依据。

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.

SNP芯片评估欧拉藏羊群体遗传多样性和遗传结构

为了解欧拉藏羊群体的遗传多样性和遗传结构,利用SNP 50K芯片检测了45只欧拉藏羊(20只公羊、25只母羊)的SNP,并进行了血样DNA提取和检测、基因组DNA的SNA分型和数据质检、群体的PCA分析、近交系数分析、亲缘关系分析、遗传距离分析、家系构建分析。结果表明,45只欧拉藏羊共得到64 734个SNP标记,质检后符合要求的数量为57 066个,其中1号染色体上有6 170个SNP位点,24号染色体上有830个位点;45只欧拉藏羊共检测到380个ROH,ROH平均近交系数为0.034,其中公羊的平均近交系数为0.052,母羊的平均近交系数为0.018,说明欧拉藏羊的近交程度不太高。从家系构建分析可知,欧拉藏羊公羊群体可分为8个家系,有5个家系公羊只有1只。后期应加强后代的扩繁和选育,以保证血统的完整。

保种场涪陵水牛及西南地区水牛品种间遗传结构与ROH分析

旨在对保种场涪陵水牛及西南地区其他沼泽型水牛品种进行群体遗传结构和连续纯合片段(ROH)分析,为涪陵水牛保种与遗传改良提供理论依据。本研究对保种场26头涪陵水牛以及1头杂交水牛(FM_HY)进行全基因组重测序,从NCBI下载了68头西南地区沼泽型水牛和7头河流型水牛的基因组重测序数据,基于所有的基因组数据获得的高质量单核苷酸多态性(SNPs)位点进行遗传结构、ROH以及近交系数的分析。全基因组重测序结果显示,涪陵水牛平均测序深度为10×,质量控制后共鉴定出14 326 437个SNPs。群体遗传结构分析显示,保种场内涪陵水牛与毗邻区域的宜宾水牛、贵州水牛、贵州白水牛、盐津水牛间具有明显的遗传结构差异,德宏水牛和滇东南水牛与上述5个品种区别均明显;当分群数量为K=6时,涪陵水牛可划分为2个类群,与毗邻区域水牛品种相比具有一类独特的群体结构。涪陵水牛、宜宾水牛、贵州水牛这3个品种间共检测到2 722个ROHs,其中涪陵水牛检测到1 593个ROHs,且1~2 Mb的短ROH片段占比达78.15%;仅在涪陵水牛群体中检测到8个大于16 Mb的长ROH片段,最长为24.56 Mb。基于ROH计算的保种场涪陵水牛平均近交系数为0.056 8,其中7头个体近交系数较高(0.062 5~0.125 0);贵州水牛和宜宾水牛的平均近交系数分别为0.034 6和0.041 0。综上,涪陵水牛保种群可分为2个类群,与毗邻区域水牛品种相比具有一类独特的群体结构;保种场内7头涪陵水牛个体存在近交风险,迫切需要加强涪陵水牛的资源保护与利用工作。

高校学术“近亲繁殖”的学科差异及其对科研产出的影响——以2所研究型高校部分学科为例

研究选取P大学(基础学科优势)与T大学(理工学科优势)两所研究型高校12个一级学科759位教师作为样本,探讨学缘关系对科研产出的影响。研究发现,T大学“近亲繁殖”情况的内部差异较大,纯正学统学者和非“近亲繁殖”学者的比重均较高;而P大学“近亲繁殖”情况的差异较小。总体而言,应用学科的“近亲繁殖”情况比基础学科更严重;工科内部学术“近亲繁殖”情况最严重,而医学领域的学缘多样性相对较好。“近亲繁殖”对科研产出有一定的积极意义,环境科学、工程力学、计算机科学等资源依赖性学科学术“近亲繁殖”对科研产出有正向促进作用,有利于提高科研产出的数量和影响力;而在基础理学与文史哲等智力依赖性学科领域,科研产出受学缘关系的影响相对较小。此外,研究还发现“非升即走”机制有利于提高科研产出质量。

Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population

Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.

Inbreeding Depression on Growth and Survival of Full-Sib Family of Manila Clam(Ruditapes philippinarum)

In present study, the inbreeding depression(ID) of growth and survival of Manila clam(Ruditapes philippinarum) was investigated at larval and juvenile stages. Nine inbred families(A_2, B_2, C_2, D_2, E_2, F_2, G_2, H_2 and I_2) were established by mating within nine full-sib families with expected inbreeding coefficient of 0.25. Inbred families showed significant differences in shell length and hatching rate of D-larvae(straight-hinged larvae). The larvae of the nine inbred families grew slower than those of control group(CG), and their ID value ranged from 0.81% ± 6.09% to 16.10% ± 1.49%. The ID value of larval survival rate varied between 27.47% ± 9.36% and 70.50% ± 13.66%. The ID was also detected for juvenile growth in A_2, B_2, C_2, and D_2, which ranged from 4.60 ± 2.21 to 17.71 ± 7.73. The A_2 family maintained the highest juvenile survival rate, whereas the other inbred families exhibited ID values varying between 62.79% ± 4.54% and 96.14% ± 0.87%. The linear relationship of estimated ID between growth and survival was negatively correlated(R =-0.434, P < 0.05). The results of this study suggested that the ID of growth was common at the larval stage but was less prevalent at juvenile stage. In contrast, the ID of survival increased from larval to juvenile stage. A better understanding of the effect of inbreeding may aid to selective breeding of Manila clam.

Elevation-related variation in the population characteristics of distylous Primula nivalis affects female fitness and inbreeding depression

The population characteristics of distylous species are highly sensitive to stochastic natural selection pressure.Therefore,populations growing under different environmental conditions may vary in floral morph ratios,potentially affecting female fitness and leading to inbreeding depression.However,the variation in offspring quality among populations as a result of inbreeding depression is poorly understood in distylous species.This study investigates variations in plant density,seed mass,seed viabilityfemale fitness,and post-dispersal inbreeding depression in both sexual morphs(long-styled and shortstyled plants)of the distylous Primula nivalis that were subjected to different pollination treatments along an elevational gradient from 1657 to 2704 m a.s.l.Population characteristics(morph plant density and ratio)and fruit set were significantly affected by sexual morph and elevation.Plant density and fruitset frequencies were lower for short-styled than for long-styled plants at 2704 m a.s.l.The seeds from the cross-pollinated flowers of both morphs were higher in quality than those of self-pollinated flowers.The female fitness of seeds from cross-pollinated flowers of both morphs was higher than that of seeds from open-pollinated and self-pollinated flowers.The female fitness of seeds from long-styled flowers was higher than that of seeds from short-styled flowers at all elevations.Inbreeding depression increased with elevation among plants with short-styled flowers but not among those with long-styled flowers.Variation in the elevation-dependent mating system might influence female fitness and affect inbreeding depression in both floral morphs.In conclusion,the low quality of seeds from short-styled flowers at high elevations might decrease short-styled flower frequency,affecting population characteristics.

Improved genetic distance-based spatial deployment can effectively minimize inbreeding in seed orchard

Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.Here,a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated,which reduced the inbreeding levels.The method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm(IAPGA)based on Python language.Using inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population,the proposed method was compared to a traditional orchard design and a distance-based design;namely,complete randomized block(RCB)and optimum neighborhood(ONA)designs,respectively.Results:With the advancement of selective breeding cycles,group separation among orchard related individuals is expected to increase.Based on the genetic distance among individuals,the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs,confirming its suitability to advanced-generation orchards where relatedness among parents is common.In the 1st,2nd,and mixed generations clonal deployment schemes,the IAPGA design produced lower inbreeding with 87.22%,81.49%,and 87.23%of RCB,and 92.78%,91.30%,and 91.67%of ONA designs,respectively.Conclusions:The IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding,and it is expected to be used in clonal deployment in seed orchards on a large-scale.Further studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards,and more assumptions should be taken into account for the optimized deployment method.

Genomic patterns of homozygosity and inbreeding depression in MurcianoGranadina goats

Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.

Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds

Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indigenous sheep breeds,which reflected their different population histories.Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding.Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds.Our findings contribute to the understanding of genetic diversity and population demography,and help design and implement breeding and conservation strategies for Chinese sheep.

Study of Swine Leukocyte Antigen Class I-3 (SLA-3) Gene for Inbreeding Wuzhishan Pig

To elucidate the structure of SLA-3 alleles on inbred line of Wuzhishan pig （WZSP） population, we examined the partial exon 1, completed exon 2, and partial exon 3 of SLA-3 loci using the reverse transcription-polymerase chain reaction （RT- PCR） and the sequencing-based method in 32 WZSPs. According to pedigree and amplification results, PCR products of 8 WZSPs were selected to clone and sequence. Nine different nucleotide sequences were obtained. After comparing the DNA and protein sequences of the WZSPs SLA-3 alleles with the published GenBank SLA sequences, it was found that the SLA-3 alleles in WZSPs were all novel, but there were very few variations among them. Comparision of SLA-3 and HLA-A protein sequences indicated that there was more sequence homology. Meanwhile, the construction of a phylogenetic tree using the nucleotide sequences of 23 SLA-3 alleles and 1 HLA-A allele represented that the WZSP population owns its unique genetics resource. In this study, the alleles of SLA-3 on WZSP group were successfully detected and analyzed, which provided the firm basis on the genotype of SLA-3 for breeding specific haplotypes WZSPs.