Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens.
Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens.
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DOI：
10.3390/biology10090876
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发表时间：
2021-09-06
期刊：
影响因子：
4.2
通讯作者：
Zinovieva NA
中科院分区：
文献类型：
--
作者：
Abdelmanova AS;Dotsev AV;Romanov MN;Stanishevskaya OI;Gladyr EA;Rodionov AN;Vetokh AN;Volkova NA;Fedorova ES;Gusev IV;Griffin DK;Brem G;Zinovieva NA
搜索推定选择性信号传导的基因组区域有助于获取有关各种物种和人群中选择史的信息。家养动物受到长期人工选择的约束，这在其基因组中留下了某些足迹，可以使用全基因组SNP筛选进行探索。我们在这里检查了两种对比鸡肉的基因组，即本地鸡蛋式俄罗斯白色和肉类的白色康沃尔。使用三个统计数据，我们在推定的选择下确定了基因组区域，包括特定品种和在两个品种之间共享的基因组区域，这些品种携带了关键候选基因的经济特征。我们的发现将有助于进一步理解家用鸡的选择史和基因组多样性，这在其生产繁殖中至关重要。
具有不同选择史的鸡肉品种中基因组足迹的比较是阐明基因组区域的强大工具，这些工具是最近和更古老的选择。在目前的工作中，我们旨在检查和比较天然鸡蛋型俄罗斯白（RW）和肉类白色康沃尔（WC）品种的人工选择的轨迹。在成对品种比较，HAPFLK分析以及对50％以上的个人共享的ROH岛的鉴定时，将三种不同的统计数据结合在一起（由FST值获得最高的0.1％SNP）。通过至少两种不同的方法检测到。 RW品种（在GGA1，GGA5，GGA8和GGA9上）和WC Breed（在GGA1，GGA1，GGA5，GGA8和GGA28上）中的每个区域中的四个都是特定于品种GGA3对于这两个品种都是常见的。大多数鉴定出的基因组区域与已知的QTL和/或候选基因重叠，包括体温，鸡蛋生产力和RW鸡的进食摄入量以及生长，肉类和car体性状，以及WC鸡的饲料效率。这些发现与他们人工选择的品种起源和历史一致。我们确定了从假定选择的11个重叠区域中检索出的188个优先候选基因，并审查了它们相对于两个品种感兴趣的表型特征的功能。 RW特异性扫描区域之一是已知的驯化基因TSHR。基因本体论和功能注释分析为扫描区域中基因的功能连贯性提供了更多见解。我们还显示了相对于这些基因组区域中的宏观色体的微色体的候选基因丰富度。我们关于RW和WC鸡的选择史的结果及其在选择下的关键候选基因，这是进一步保护其基因组多样性和有效繁殖的深刻信息。
The search for genomic regions of putative selective signaling is instrumental in obtaining information about selection history in various species and populations. Domestic animals are subject to long-term artificial selection that leaves certain footprints in their genomes one can explore using genome-wide SNP screen. We examined here genomes of two contrasting chicken breeds, the native egg-type Russian White and meat-type White Cornish. Using three statistics, we identified genomic regions under putative selection, both breed-specific and shared between two breeds, that harbor key candidate genes for economically important traits. Our findings will be useful in further understanding selection history and genomic diversity in domestic chickens that would be pivotal in their productive breeding. Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.
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DOI：
10.1186/s12711-018-0399-5
发表时间：
2018-05-24
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Deniskova TE;Dotsev AV;Selionova MI;Kunz E;Medugorac I;Reyer H;Wimmers K;Barbato M;Traspov AA;Brem G;Zinovieva NA
通讯作者：
Zinovieva NA
DOI：
10.1101/sqb.2003.68.69
发表时间：
2003-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
Fan, JB;Oliphant, A;Chee, MS
通讯作者：
Chee, MS
俄罗斯白蛋鸡催乳素和多巴胺受体 D2 基因插入缺失的遗传变异及其与尿囊羊水产量的关系
DOI：
10.15832/ankutbd.483561
发表时间：
2020-01-01
影响因子：
0.9
作者：
Dementieva, Natalia, V;Fedorova, Elena S.;Romanov, Michael N.
通讯作者：
Romanov, Michael N.
影响因子：
2.9
作者：
Fu W;Lee WR;Abasht B
通讯作者：
Abasht B
DOI：
10.1186/1297-9686-45-42
发表时间：
2013-10-29
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Ferenčaković M;Sölkner J;Curik I
通讯作者：
Curik I