Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice.
Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice.
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基于 Bin 的全基因组关联研究揭示了使用 4 路 MAGIC 群体改善水稻外观质量的优异等位基因
DOI：
10.1016/j.jare.2020.08.001
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发表时间：
2021-03
影响因子：
10.7
通讯作者：
Xing Y
中科院分区：
文献类型：
--
作者：
Ayaad M;Han Z;Zheng K;Hu G;Abo-Yousef M;Sobeih SES;Xing Y
四向多亲本群体克服了双亲结构的局限性。
单核苷酸多态性（SNP）与bin全基因组关联分析（bin - GWAS）相结合，为数量性状基因座（QTL）定位提供了强大的工具。
qPGWC8.2包含一个预测的与水稻垩白品质相关的新基因。
多亲本群体为我们提供了鉴定控制某一性状的优良等位基因以用于遗传改良的机会。与基于单核苷酸多态性水平的全基因组关联分析（SNP - GWAS）相比，基于bin水平的全基因组关联分析（bin - GWAS）有望在QTL定位方面更具效力。
本研究旨在通过SNP - GWAS和bin - GWAS评估控制水稻粒形外观品质的QTL的遗传效应，比较它们在QTL定位中的效力，并从4个亲本中鉴定出所有检测到的QTL的优良等位基因，以用于遗传改良。
在两种环境下种植了一个四向多亲本高级世代互交（MAGIC）群体及其四个亲本，以剖析水稻粒形外观品质的遗传基础。同时进行了SNP - GWAS和bin - GWAS用于QTL定位。通过对4个亲本的bin/等位基因进行多重比较来鉴定优良等位基因。
SNP - GWAS和bin - GWAS分别鉴定出了16个和20个与粒形外观品质相关的QTL。一个微小垩白QTL qPGWC8.2/qDEC8被定位到一个30千碱基对的基因组区域，其中OsMH_08T0121900是潜在的候选基因，因为其编码的蛋白质——葡聚糖内 - 1,3 - β - 葡糖苷酶前体参与淀粉和蔗糖代谢途径。GS3、GL3.1、GW5、GW7、Chalk5以及两个QTL的优良亲本等位基因几乎都由优质亲本赛普里斯（Cypress）和粤晶丝苗（YJSM）携带，而劣质亲本桂朝2号（GC2）则总是携带劣质等位基因。粒形和垩白性状品质最优的前五个重组自交系均携带优良等位基因的基因组合。
鼓励将SNP - GWAS和bin - GWAS两种方法与MAGIC群体联合用于QTL定位。qPGWC8.2/qDEC8是一个与垩白密切相关的新候选基因。本研究鉴定出了GS3、GW5、GL3.1、GW7、Chalk5和qPGWC8.2的优良等位基因，这些优良等位基因的聚合有助于改善水稻外观品质。
4-way Multiparental population covered the limitations of the biparental structure. The combination of SNP and bin-GWAS showed a powerful tool for QTL mapping. qPGWC8.2 harbored a novel predicted gene for rice chalkiness quality. The multiparental population provides us the chance to identify superior alleles controlling a trait for genetic improvement. Genome wide association studies at bin level (bin-GWAS) are expected to be more power in QTL mapping than GWAS at SNP level (SNP-GWAS). This study is to estimate genetic effects of QTL conferring grain appearance quality in rice by SNP-GWAS and bin-GWAS, compare their power in QTL mapping and identify the superior alleles of all detected QTL from 4 parents for genetic improvement. A 4-way MAGIC population and its four founders were cultivated in two environments to dissect the genetic basis of rice grain appearance quality. Both SNP-GWAS and bin-GWAS were conducted for QTL mapping. Multiple comparison among 4 parental bin/alleles was used to identify the superior alleles. A total of 16 and 20 QTL associated with grain appearance quality were identified by SNP- and bin-GWAS, respectively. A minor chalkiness QTL qPGWC8.2/qDEC8 was assigned to a 30-kb genomic region, in which OsMH_08T0121900 is the potential candidate gene because its encoded protein, glucan endo-1,3-beta-glucosidase precursor is involved in the starch and sucrose metabolism pathway. The superior parental alleles for GS3, GL3.1, GW5, GW7, and Chalk5 and two QTLs were almost carried by the high-quality parents Cypress and Yuejingsimiao (YJSM), while the poor-quality parent Guichao-2 (GC2) always carried the inferior alleles. The top five recombinant inbred lines with the highest quality of grain shape and chalkiness traits all carried gene combinations of superior alleles. Both SNP- and bin-GWAS methods are encouraged for joint QTL mapping with MAGIC population. qPGWC8.2/qDEC8 is a novel candidate gene strongly associated with chalkiness. The superior alleles of GS3, GW5, GL3.1, GW7, Chalk5 and qPGWC8.2 were identified, and the pyramiding of these superior alleles is helpful to improve rice appearance quality.
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DOI：
10.1186/s12284-018-0236-z
发表时间：
2018-08-02
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Dong Q;Zhang ZH;Wang LL;Zhu YJ;Fan YY;Mou TM;Ma LY;Zhuang JY
通讯作者：
Zhuang JY
影响因子：
4.5
作者：
Dong H;Zhao H;Li S;Han Z;Hu G;Liu C;Yang G;Wang G;Xie W;Xing Y
通讯作者：
Xing Y
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：
11.4
作者：
Guo, Tao;Liu, Xiaolu;Wan, Jianmin
通讯作者：
Wan, Jianmin
影响因子：
7
作者：
Huang, Xuehui;Feng, Qi;Han, Bin
通讯作者：
Han, Bin