Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

Birth weight(BW) and days to 100 kg(D100) are important economic traits that are both affected by polygenes. However, the genetic architecture of these quantitative traits is still elusive. Genotyping-by-sequencing(GBS) data containing a large number of single nucleotide polymorphisms(SNPs) have become a powerful tool in genomic analysis. To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology. After quality control, 279 787 SNPs were generated for subsequent genome-wide association study(GWAS). A total of 30 genome-wide SNPs(P1.79 E–07) were identified for D100. Furthermore, a total of 22 and 2 suggestive SNPs(P3.57 E–06) were detected for D100 and BW, respectively. Of these, one locus located on SSC12(position: 46 226 512 bp) were evaluated to affect both BW and D100 in Yorkshire pigs, indicating the pleiotropism in different traits. Considering the function of candidate genes, two genes, NSRP1 and DOCK7, were suggested as the most promising candidate genes involved in growth traits. Thus, use of GBS is able to identify novel variants and potential candidate genes for BW and D100, and provide an opportunity for improving pig growth traits using genomic selection in pigs.     

Integration of association and computational methods reveals functional variants of LEPR gene for abdominal fat content in chickens

Leptin receptor(LEPR) plays a vital role in obesity in humans and animals. The objective of this study is to assess LEPR functional variants for chicken adipose deposition by integration of association and in-silico analysis using a unique chicken population, the Northeast Agricultural University broiler lines divergently selected for abdominal fat content(NEAUHLF). Five online bioinformatics tools were used to predict the functionality of the single nucleotide polymorphisms(SNPs) in coding region. Further, the possible structure–function relationship of high confidence SNPs was determined by bioinformatics analyses, including the conservation and stability analysis based on amino acid residues, prediction of protein ligand-binding sites, and the superposition of protein tertiary structure. Meanwhile, we analyzed the association between abdominal fat traits and 20 polymorphisms of chicken LEPR gene. The integrated results showed that rs731962924(N867 I) and rs13684622(C1002 R) could lead to striking changes in the structure and function of proteins, of which rs13684622(C1002 R) was significantly associated with abdominal fat weight(AFW, P=0.0413) and abdominal fat percentage(AFP, P=0.0260) in chickens. Therefore, we are of the opinion that rs13684622(C1002 R) may be an essential functional SNP affecting chicken abdominal fat deposition, and potentially applied to improvement of broiler abdominal fat in molecular marker-assisted selection(MAS) program. Additionally, the coupling of association with computer electronic predictive analysis provides a new avenue to identify important molecular markers for breeders.     

Whole genome SNPs among 8 chicken breeds enable identification of genetic signatures that underlie breed features

Many different chicken breeds are found around the world, their features vary among them, and they are valuable resources. Currently, there is a huge lack of knowledge of the genetic determinants responsible for phenotypic and biochemical properties of these breeds of chickens. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved chicken breeds. The whole-genomes of 140 chickens from 7 Shandong native breeds and 20 introduced recessive white chickens from China were re-sequenced. Comparative population genomics based on autosomal single nucleotide polymorphisms (SNPs) revealed geographically based clusters among the chickens. Through genome-wide scans for selective sweeps, we identified thyroid stimulating hormone receptor (TSHR, reproductive traits, circadian rhythm), erythrocyte membrane protein band 4.1 like 1 (EPB41L1, body size), and alkylglycerol monooxygenase (AGMO, aggressive behavior), as major candidate breed-specific determining genes in chickens. In addition, we used a machine learning classification model to predict chicken breeds based on the SNPs significantly associated with recourse characteristics, and the prediction accuracy was 92%, which can effectively achieve the breed identification of Laiwu Black chickens. We provide the first comprehensive genomic data of the Shandong indigenous chickens. Our analyses revealed phylogeographic patterns among the Shandong indigenous chickens and candidate genes that potentially contribute to breed-specific traits of the chickens. In addition, we developed a machine learning-based prediction model using SNP data to identify chicken breeds. The genetic basis of indigenous chicken breeds revealed in this study is useful to better understand the mechanisms underlying the resource characteristics of chicken.     

GHRL基因5′侧翼区多态性对鸡生长和屠体性状的影响

 【目的】分析GHRL基因5′侧翼区变异与鸡生长和屠体性状的相关性。【方法】以杏花鸡×隐性白洛克鸡F2代资源群体和2个随机群体为材料,利用PCR产物直接测序方法鉴别GHRL基因5′侧翼区包括A-2220C位点在内的6个SNPs在群体中的多态性,构建单倍型,分析各SNP基因型和单倍型与鸡生长、屠体性状,以及与腺胃GHRL基因mRNA表达量和血浆GHRL活性蛋白含量的相关性,对鸡GHRL基因5′侧翼区的A-2220C位点进行凝胶阻滞电泳,以探讨该区段对基因转录的作用。【结果】标记-性状关联分析表明A-2220C仅与初生重显著相关（P＜0.05）,AA基因型个体初生重大于CC和AC基因型个体,差异显著（P＜0.05）;C-2399Del与56日龄体重、0—4周日增重、胸肌重、翅重显著相关（P＜0.05）,C Del基因型杂合子优势明显,与其它基因型差异显著（P＜0.05）。构建单倍型分析表明单倍型分别与42日龄体重、70日龄体重、0—4周日增重、4—8周日增重、屠体重、半净膛重、全净膛重和胸肉重显著相关（P＜0.05）;与初生重、21日体重、28日体重、35日体重、49日龄体重、56日龄体重、宰前活重等极显著相关（P＜0.01）,单倍型组合H3H4（CCAAAC\CCAACDel）是各个显著相关性状中均值最高的优势单倍型组合。EMSA电泳发现含A等位基因的DNA片段能与转录因子特异的结合,初步证实本试验扩增片段对基因的转录存在一定作用。【结论】GHRL基因与鸡生长和屠体性状存在显著相关性。     

I-FABP基因侧翼区多态性与鸡生长和胴体组成性状的相关研究

本研究以东北农业大学高、低腹脂双向选择品系第9世代肉仔鸡为试验材料,利用PCR-RFLP法对鸡肠型脂肪酸结合蛋白基因进行单核苷酸多态性(SNPs)检测,分析该基因多态性与鸡生长和胴体组成性状的关系。统计分析结果表明,该基因c.*822G>A突变位点不同基因型对肉仔鸡5周龄、7周龄体重和屠体重有显著影响(P<0.05),对出生重、1周龄和3周龄体重有一定的影响(P<0.2)。AA基因型个体的5周龄、7周龄体重和屠体重显著高于AG和GG基因型个体(P<0.05)。本研究首次推测I-FABP基因可能是影响鸡体重的主效基因或与影响该性状的主效基因紧密连锁。     

Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F2 chicken population

Improving the production of broiler chicken meat has been a goal of broiler breeding programs worldwide for many years. However, the genetic architectures of skeletal muscle production traits in chickens have not yet been fully elucidated. In the present study, a total of 519 F₂ birds, derived from a cross of Arbor Acres broiler and Baier layer, were re-sequenced (26 F₀ individuals were re-sequenced at a 10-fold depth; 519 F₂ individuals were re-sequenced at a 3-fold depth) and the coupling of genome-wide association study (GWAS) and selection signatures (F_ST (fixation index) and θ_π (nucleotide diversity)) was carried out to pinpoint the associated loci and genes that contribute to pectoral muscle weight (PMW) and thigh muscle weight (TMW). A total of 7 890 258 single nucleotide polymorphisms (SNPs) remained to be analyzed after quality control and imputation. The integration of GWAS and selection signature analyses revealed that genetic determinants responsible for skeletal muscle production traits were mainly localized on chromosomes 1 (168.95–172.43 Mb) and 4 (74.37–75.23 Mb). A total of 17 positional candidate genes (PCGs) (LRCH1, CDADC1, CAB39L, LOC112531568, LOC112531569, FAM124A, FOXO1, NBEA, GPALPP1, RUBCNL, ARL11, KPNA3, LHFP, GBA3, LOC112532426, KCNIP4, and SLIT2) were identified in these regions. In particular, KPNA3 and FOXO1 were the most promising candidates for meat production in chickens. These findings will help enhance our understanding of the genetic architecture of chicken muscle production traits, and the significant SNPs identified could be promising candidates for integration into practical breeding programs such as genome-wide selection (GS) to improve the meat yield of chickens.     

Dissecting the genetic basis of maize deep-sowing tolerance by combining association mapping and gene expression analysis

Deep-sowing is an important method for avoiding drought stress in crop species, including maize. Identifying candidate genes is the groundwork for investigating the molecular mechanism underlying maize deep-sowing tolerance. This study evaluated four traits (mesocotyl length at 10 and 20 cm planting depths and seedling emergence rate on days 6 and 12) related to deep-sowing tolerance using a large maize population containing 386 inbred lines genotyped with 0.5 million high-quality single nucleotide polymorphisms (SNPs). The genome-wide association study detected that 273 SNPs were in linkage disequilibrium (LD) with the genetic basis of maize deep-sowing tolerance. The RNA-sequencing analysis identified 1 944 and 2 098 differentially expressed genes (DEGs) in two comparisons, which shared 281 DEGs. By comparing the genomic locations of the 273 SNPs with those of the 281 DEGs, we identified seven candidate genes, of which GRMZM2G119769 encoded a sucrose non-fermenting 1 kinase interactor-like protein. GRMZM2G119769 was selected as the candidate gene because its homologs in other plants were related to organ length, auxin, or light response. Candidate gene association mapping revealed that natural variations in GRMZM2G119769 were related to phenotypic variations in maize mesocotyl length. Gene expression of GRMZM2G119769 was higher in deep-sowing tolerant inbred lines. These results suggest that GRMZM2G119769 is the most likely candidate gene. This study provides information on the deep-sowing tolerance of maize germplasms and identifies candidate genes, which would be useful for further research on maize deep-sowing tolerance.     

鸡lmbr1基因内含子多态与趾型的关联

 【目的】多趾是丝羽乌骨鸡的品种特征之一，但其多趾发生的分子机制尚未知。Lmbr1基因是人和鼠轴前多趾的关键候选基因，其同源基因是否是鸡多趾表型的关键候选基因值得研究。【方法】本研究以多趾的丝羽乌骨鸡和四趾的白洛克肉鸡杂交建立的资源家系为研究素材，采用直接测序和PCR-SSCP相结合的方法进行了鸡lmbr1基因内含子13的克隆、多态分析及其在不同物种的序列保守性比较、单体型分析及单核苷酸多态与趾型的关联分析。【结果】从内含子13检测到4个SNPs，发现这些单核苷酸多态构成的单体型在丝羽乌骨鸡和白洛克肉鸡间的分布呈现明显的差异，PCR-SSCP基因型在资源家系亲代和F2代均呈现与趾型的显著关联。【结论】 鸡lmbr1基因内含子13变异与调控鸡多趾表型的特异性位点紧密连锁，鸡lmbr1基因应是鸡多趾表型的重要候选基因，今后应进一步加大鸡lmbr1基因全基因组水平和其临近区域基因的检测。     

Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica rice (Oryza sativa L.) in Northeast China

Milling and appearance quality are important contributors to rice grain quality. Abundant genetic diversity and a suitable environment are crucial for rice improvement. In this study, we investigated the milling and appearance quality-related traits in a panel of 200 japonica rice cultivars selected from Liaoning, Jilin and Heilongjiang provinces in Northeast China. Pedigree assessment and genetic diversity analysis indicated that cultivars from Jilin harbored the highest genetic diversity among the three geographic regions. An evaluation of grain quality indicated that cultivars from Liaoning showed superior milling quality, whereas cultivars from Heilongjiang tended to exhibit superior appearance quality. Single- and multi-locus genome-wide association studies (GWAS) were conducted to identify loci associated with milling and appearance quality-related traits. Ninety-nine significant single-nucleotide polymorphisms (SNPs) were detected. Three common SNPs were detected using the mixed linear model (MLM), mrMLM, and FASTmrMLM methods. Linkage disequilibrium decay was estimated and indicated three candidate regions (qBRR-1, qBRR-9 and qDEC-3) for further candidate gene analysis. More than 300 genes were located in these candidate regions. Gene Ontology (GO) analysis was performed to discover the potential candidate genes. Genetic diversity analysis of the candidate regions revealed that qBRR-9 may have been subject to strong selection during breeding. These results provide information that will be valuable for the improvement of grain quality in rice breeding.     

KDR等6个基因多态性与鸡生长和体组成性状的相关研究

以东北农业大学高、低脂肉鸡双向选择品系第14世代群体(NEAUHLFG14)和AA肉鸡商业随机群体(AA群体)为试验材料,利用PCR-RFLP对鸡腹脂性状的全基因组关联分析(GWAS)鉴定出6个多态位点进行单核苷酸多态性(SNPs)检测,分析这些位点的多态性与鸡生长和体组成性状的关系。结果表明,在NEAUHLFG14中KDR基因的rs14483313位点多态性对腹脂重(AFW)和腹脂率(AFP)有显著影响(P<0.05),TUSC3基因的rs13548811位点对鸡后期体重有影响,EXOC1基因的GGaluGA263078位点在两个群体中都对7周龄体重(BW7)有显著影响(P<0.05)。TUSC3、PPAT、EXOC1和KIAA1211基因的突变位点对NEAUHLFG14极低密度脂蛋白(VLDL)浓度有显著影响(P<0.05),结果显示,6个基因可能是影响鸡腹脂性状的重要基因,但多态位点是否为功能性位点仍需进一步验证。     

甜玉米籽粒体积和粒重的全基因组关联分析

为挖掘控制甜玉米籽粒体积和粒重的相关基因,2017—2019年,以209份甜玉米自交系构成的关联群体为材料,测定干籽粒的体积和粒重,结合全基因组重测序(De novo sequencing)获得的980万个单核苷酸多态性(Single-nucleotide polymorphism,SNP)标记,采用GLM模型进行全基因组关联分析。结果表明,甜玉米籽粒体积变异范围为0.06~0.15 mL,变异倍数为2.5倍,单粒重变异范围为0.08~0.17 g,变异倍数为2.1倍,均符合正态分布。共检测到15个SNP位点与籽粒体积或粒重显著关联,分别解释籽粒体积55.7%和粒重52.1%的表型变异,其中4个位点和普通玉米报道的QTL重叠,其余11个是新鉴定的位点,通过基因注释发现大部分候选基因为转录因子等调控基因。此外,首次检测到Br2(矮化基因2)与籽粒体积、粒重两性状均显著关联,并且籽粒体积和粒重均随着该基因表达量的升高而增加。     

鸡胸腺重和脾脏重性状的全基因组关联

【目的】全基因组关联分析（genome-wide association study,GWAS）是复杂性状和疾病相关基因定位的新策略。【方法】试验利用鸡60K SNP芯片对来自50个公鸡家系的728只北京油鸡进行SNP分型检测,采用全基因组关联分析方法对影响100日龄胸腺重和脾脏重的基因进行定位研究。【结果】结果发现24个达5%全基因组水平显著的位点,与100日龄胸腺重和脾脏重显著相关,并在这些位点附近发现Janus kinase 1（JAK1）、 zinc finger DHHC-type containing 8（ZDHHC8）、vav 3 guanine nucleotide exchange factor（VAV3）、SATB homeobox 1（SATB1）等候选基因;84个与这两个性状潜在关联同时达到5%染色体水平显著的位点。【结论】利用GWAS分析策略筛选和鉴定的重要突变位点及候选基因,将为揭示鸡免疫器官发育的分子调控机制和抗病育种分子标记辅助选择提供必要的分子基础。     

鸡ApoB基因多态位点与生长和体组成性状的相关性研究

载脂蛋白B(Apolipoprotein B,ApoB)是血浆脂蛋白的主要成分,对脂类代谢具有重要的调控作用。本研究以东北农业大学高、低腹脂双向选择品系第9世代仔鸡为试验材料,对鸡ApoB基因进行SNP检测,分析ApoB基因多态性与生长和体组成性状的关系。根据鸡基因组测序结果提供的SNP,发现鸡ApoB基因5′调控区的-112A>G、3′调控区的9 bp插入缺失以及exon26上T>G的同义突变3个突变位点在研究群体中存在多态性。统计分析结果表明,5′调控区的-112A>G突变位点和3′调控区的插入缺失突变位点对7周龄体重和屠体重有显著影响(P<0.05),exon26上T>G对屠体重有显著影响(P<0.05),对7周龄体重有一定的影响(P<0.01)。本研究首次推测ApoB基因可能是影响鸡体重的主效基因或与影响该性状的主效基因紧密连锁。     

牦牛SMAD1基因第1外显子SNPs检测及与生长性状的关联分析

研究牦牛 SMAD1基因第1外显子SNPs与生长性状的关系，寻找与牦牛生长性状相关的分子标记。采用DNA测序和单倍型分型技术，对青海牦牛 SMAD1基因进行SNPs检测及其基因分型、连锁不平衡和单倍型分析，并对多态位点的基因型及组合单倍型与牦牛生长性状的关联性进行分析。结果发现， SMAD1在第1外显子上存在5个突变位点，其中，g.35084C>T、g.35111C>T和g.35333G>A均存在2种基因型，g.35171G>A和g.35312C>T均存在3种基因型。连锁不平衡分析发现5个位点间不存在强的连锁不平衡效应，单倍型分析发现存在6种不同的单倍型，其中单倍型Hap3的发生频率最高。关联性分析表明，g.35084C>T位点与胸围显著相关，g.35111C>T位点与体斜长、胸围显著相关，g.35171G>A和g.35312C>T位点与体质量、体高、体斜长和胸围显著相关，g.35333G>A位点与胸围、体高显著相关。通过基因型组合发现，4种组合单倍型均与牦牛生长性状有着显著或极显著相关，且H3H6可能是影响牦牛生长性状的最优...     

鸡Myogenin基因单核苷酸多态检测及群体遗传分析

肌纤维在决定肌肉生长和肉质方面起主要作用,并受到MyoD基因家族的调控。该家族基因编码螺旋-环-螺旋蛋白。以鸡Myogenin基因为候选基因,通过PCR-SSCP分析该基因5′调控区的变异。结果表明,在鸡Myogenin基因5′调控区存在3处SNPs,这些SNPs产生的不同基因型及等位基因在7个品种鸡间分布存在极显著的差异(P<0.001)。推测该基因的变异对鸡生长发育可能有一定的影响。     

GDFs基因家族候选基因对崇仁麻鸡生长性状的影响

利用崇仁麻鸡差异性状的重测序结果,将生长分化因子(GDFs)基因家族作为候选基因,筛选与崇仁麻鸡生长性状相关的多态位点。结果发现,GDF-2、GDF-8和GDF-10基因的多态位点对崇仁麻鸡的生长性状有着显著或极显著的影响。单倍型分析结果显示,GDF-2和GDF-10基因的单倍型H3H3为劣势单倍型组合可以选择淘汰。研究结果表明,GDFs基因家族候选基因对崇仁麻鸡的生长性状有一定的影响。     

惠阳胡须鸡IGF-Ⅰ和GHRL基因多态性研究

以IGF-Ⅰ和GHRL基因为惠阳胡须鸡生长性状的候选基因,通过测序、酶切等方法对93日龄惠阳胡须鸡IGF-Ⅰ和GHRL基因多态性进行分析,并用GLM模型分析基因型与体质量的关联性。结果表明:IGF-Ⅰ基因在第181位发生碱基突变,A突变为G,属于同义突变,BsmⅠ酶切分析发现,IGF-Ⅰ基因只有1种基因型,表明该位点在胡须鸡保种群中已经纯合;GHRL基因在第124位发生碱基突变,T突变为G,改变了酶切位点,通过pfl MⅠ酶切分析发现,GHRL基因有3种基因型,即AA型、AB型和BB型。统计结果表明,93日龄惠阳胡须鸡3种基因型个体间体质量无显著差异。     

Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population

Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large White×Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip and were phenotyped for 10 traits, specifically, backfat thickness (6-7 libs), carcass length, carcass weight, foot weight, head weight, heart weight, leaf fat weight, liver weight, lung weight and slaughter body weight. The genome-wide association study (GWAS) was assessed by Genome Wide Rapid Association using the mixed model and regression-genomic control approach. A total of 31 single nucleotide polymorphisms (SNPs) (with the most significant SNP being MARC0033464, P value=6.80×10-13) were located in a 9.76-Mb (31.24-41.00 Mb) region on SSC7 and were found to be significantly associated with one or more carcass traits and organ weights. High percentage of phenotypic variance explanation was observed for each trait ranging from 31.21 to 67.42%. Linkage analysis revealed one haplotype block of 495 kb, in which the most significant SNP being MARC0033464 was contained, on SSC7 at complete linkage disequilibrium. Annotation of the pig reference genome suggested 6 genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in this candidate linkage disequilibrium (LD) interval. Functional analysis indicated that the HMGA1 gene presents the prime biological candidate for carcass traits and organ weights in pig, with potential application in breeding programs.     

蛋鸡资源群体的盲肠长度全基因组关联分析

【目的】盲肠是鸡进一步消化和吸收养分,尤其是纤维的器官,对鸡的生长及后期产蛋都具有重要作用,因此鸡的盲肠长度是一个重要的生理指标.【方法】通过对白来航鸡与东乡绿壳蛋鸡杂交所得F2代个体的盲肠长度进行测量,并运用单核苷酸多态性(SNP)芯片检测其基因分型,根据SNP检测数据运用SAS进行遗传评估,并用全基因组混合模型关联算法(GEMMA)进行单变量全基因组关联分析(GWAS).【结果】结果显示,盲肠长度表现出中等遗传力(0.39).GWAS鉴定出54个SNP与盲肠的长度显著相关,且1号染色体170 Mb附近对于盲肠长度来说是一个重要区域.在这个区域,覆盖26个SNP位点的18个基因被定为候选基因,其中2个分别在编码序列(CDS)和3'非翻译区(3'UTR),对应于NHLRC3和SIAH3,它们可能是影响盲肠长度的重要SNP位点和基因.【结论】利用GWAS筛选并鉴定出和鸡盲肠长度相关联的SNP位点及基因,将为揭示蛋鸡盲肠发育的机制和分子育种提供基础.