Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia (O. niloticus).
Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia (O. niloticus).
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DOI：
10.3389/fgene.2018.00472
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发表时间：
2018
影响因子：
3.7
通讯作者：
Kent M
中科院分区：
文献类型：
--
作者：
Joshi R;Árnyasi M;Lien S;Gjøen HM;Alvarez AT;Kent M
尽管罗非鱼是世界上第二大水产养殖物种，占2015年全球产量的7.4%，但罗非鱼水产养殖缺乏SNP阵列和高密度连锁图谱等基因组工具来提高选择准确性和加速遗传进步。在本文中，我们描述了一个基因分型阵列包含超过58,000个SNPs的尼罗罗非鱼（Oreochromis niloticus）的发展。从来自Genomar菌株的商业群体的32个个体的全基因组重测序中鉴定SNP，并使用Orenil1.1基因组组装作为参考序列，基于多态性信息含量和基因组上的物理分布选择SNP阵列。通过对4991个个体进行基因分型来评估SNP性能，其中包括属于41个全同胞家庭的689个后代，其揭示了43，588个SNP的高质量基因型数据。使用Lepmap 2构建初步遗传连锁图，Lepmap 2又与来自O_niloticus_UMD1基因组组装的信息整合，以产生包含分布在22个连锁群（LG）中的40，186个SNP的整合的物理和遗传连锁图。大约三分之一的LGs显示出不同性别之间的重组率，雌性比雄性图谱大1.2倍（分别为1632.9至1359.6 cM），大多数LGs显示出S形重组谱。最后，性别决定基因座被定位到LG 23上的40.53 cM位置，在抗苗勒管激素（amh）基因附近。这些新的资源有可能在应用基因组选择时极大地影响和提高遗传增益，并克服尼罗罗非鱼入侵测量性状的有效选择的困难。
Despite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper, we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia (Oreochromis niloticus). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and were selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O_niloticus_UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups (LGs). Around one-third of the LGs showed a different recombination rate between sexes, with the female being greater than the male map by a factor of 1.2 (1632.9 to 1359.6 cM, respectively), with most LGs displaying a sigmoid recombination profile. Finally, the sex-determining locus was mapped to position 40.53 cM on LG23, in the vicinity of the anti-Müllerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasively measured traits in Nile tilapia.
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DOI：
10.1534/g3.118.200053
发表时间：
2018-03-28
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Barría A;Christensen KA;Yoshida GM;Correa K;Jedlicki A;Lhorente JP;Davidson WS;Yáñez JM
通讯作者：
Yáñez JM
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
4.4
作者：
Correa K;Lhorente JP;López ME;Bassini L;Naswa S;Deeb N;Di Genova A;Maass A;Davidson WS;Yáñez JM
通讯作者：
Yáñez JM
全基因组协会研究（GWAS）关于大西洋鲑鱼（Salmo Salar）性成熟时的增长率和年龄。
影响因子：
3.7
作者：
Gutierrez AP;Yáñez JM;Fukui S;Swift B;Davidson WS
通讯作者：
Davidson WS