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使用全基因组序列的基因组关联研究在瑞士褐牛中的生育和产犊性状。

Genome-wide association studies of fertility and calving traits in Brown Swiss cattle using imputed whole-genome sequences.

机构信息

Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland.

School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland.

出版信息

BMC Genomics. 2017 Nov 25;18(1):910. doi: 10.1186/s12864-017-4308-z.

DOI:10.1186/s12864-017-4308-z
PMID:29178833
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5702100/
Abstract

BACKGROUND: The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic data available. Functional traits such as fertility and calving traits have been included in routine genomic estimation of breeding values making large quantities of phenotypic data available for these traits. This data was used to investigate the genetics underlying fertility and calving traits and to identify potentially causative genomic regions and variants. We performed genome-wide association studies for 13 functional traits related to female fertility as well as for direct and maternal calving ease based on imputed whole-genome sequences. Deregressed breeding values from ~1000-5000 bulls per trait were used to test for associations with approximately 10 million imputed sequence SNPs. RESULTS: We identified a QTL on BTA17 associated with non-return rate at 56 days and with interval from first to last insemination. We found two significantly associated non-synonymous SNPs within this QTL region. Two more QTL for fertility traits were identified on BTA25 and 29. A single QTL was identified for maternal calving traits on BTA13 whereas three QTL on BTA19, 21 and 25 were identified for direct calving traits. The QTL on BTA19 co-localizes with the reported BH2 haplotype. The QTL on BTA25 is concordant for fertility and calving traits and co-localizes with a QTL previously reported to influence stature and related traits in Brown Swiss dairy cattle. CONCLUSION: The detection of QTL and their causative variants remains challenging. Combining comprehensive phenotypic data with imputed whole genome sequences seems promising. We present a QTL on BTA17 for female fertility in dairy cattle with two significantly associated non-synonymous SNPs, along with five additional QTL for fertility traits and calving traits. For all of these we fine mapped the regions and suggest candidate genes and candidate variants.

摘要

背景：随着基因组学的最新发展，定量性状基因座的检测速度加快。基因组选择的引入结合测序工作，使得大量基因型数据可用。功能性状，如繁殖力和分娩性状，已被纳入常规的基因组估计育种值，为这些性状提供了大量的表型数据。利用这些数据，我们对繁殖力和分娩性状的遗传基础进行了研究，并确定了潜在的因果基因组区域和变体。我们对与雌性繁殖力相关的 13 个功能性状以及直接和母体分娩轻松度进行了全基因组关联研究，这些性状都是基于已估计的全基因组序列进行的。对每个性状的约 1000-5000 头公牛的去分化育种值进行了检测，以检验与约 1000 万个已估计序列 SNP 的关联。

结果：我们在 BTA17 上发现了一个与 56 天返情率和首次到最后一次配种间隔相关的 QTL。在这个 QTL 区域内发现了两个显著相关的非同义 SNP。在 BTA25 和 29 上还发现了两个与繁殖力性状相关的 QTL。在 BTA13 上发现了一个与母体分娩性状相关的单个 QTL，而在 BTA19、21 和 25 上发现了三个与直接分娩性状相关的 QTL。BTA19 上的 QTL 与报道的 BH2 单倍型重合。BTA25 上的 QTL 与繁殖力和分娩性状一致，并与先前报道的影响瑞士褐牛奶牛体型和相关性状的 QTL 重合。

结论：QTL 及其致病变体的检测仍然具有挑战性。将全面的表型数据与已估计的全基因组序列相结合似乎很有前途。我们在奶牛 BTA17 上发现了一个与雌性繁殖力相关的 QTL，有两个显著相关的非同义 SNP，还有五个与繁殖力和分娩性状相关的其他 QTL。对于所有这些 QTL，我们都对其进行了精细定位，并提出了候选基因和候选变体。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/9919b45c6ff4/12864_2017_4308_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/88a7663480a5/12864_2017_4308_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/0b0e0811fd92/12864_2017_4308_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/3bd65ac42538/12864_2017_4308_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/d5d647e2baf7/12864_2017_4308_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/5f59edd68946/12864_2017_4308_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/9919b45c6ff4/12864_2017_4308_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/88a7663480a5/12864_2017_4308_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/0b0e0811fd92/12864_2017_4308_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/3bd65ac42538/12864_2017_4308_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/d5d647e2baf7/12864_2017_4308_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/5f59edd68946/12864_2017_4308_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d501/5702100/9919b45c6ff4/12864_2017_4308_Fig6_HTML.jpg

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