Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz)

文献类型： 外文期刊

第一作者： Zhang, Shengkui

作者： Zhang, Shengkui;Zhang, Shengkui;Chen, Xin;Lu, Cheng;Zou, Meiling;Feng, Subin;Pei, Jinli;Liu, Chen;Zhou, Xincheng;Ma, Ping'an;Xia, Zhiqiang;Wang, Wenquan;Ye, Jianqiu;Lu, Kundian;Li, Zhaogui;Liu, Cuijuan;Liao, Qi

作者机构：

关键词： Manihot esculenta Crantz; single-nucleotide polymorphism (SNP); genetic diversity; population structure; genome-wide association analysis (GWAS)

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2018 年 9 卷

页码：

收录情况： SCI

摘要： Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 x 10(4) for all sampled landraces. This average nucleotide diversity was 1.97 x 10(4), 1.01 x 10(4), and 1.89 x 10(4) for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about similar to 8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes. 13G023300, Manes. 16G000800, Manes. 02G154700, Manes. 02G192500, and Manes. 09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes. 05G164500, Manes. 05G164600, Manes. 04G057300, Manes. 01G202000, and Manes. 03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.

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