Ayaad Mohammed, Han Zhongmin, Zheng Kou, Hu Gang, Abo-Yousef Mahmoud, Sobeih Sobeih El S, Xing Yongzhong
National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China.
Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal 13759, Egypt.
J Adv Res. 2020 Aug 11;28:183-194. doi: 10.1016/j.jare.2020.08.001. eCollection 2021 Feb.
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 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 and 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. q is a novel candidate gene strongly associated with chalkiness. The superior alleles of and were identified, and the pyramiding of these superior alleles is helpful to improve rice appearance quality.
多亲本品系群体为我们提供了识别控制性状的优良等位基因以进行遗传改良的机会。预计在QTL定位中，基于bin水平的全基因组关联研究（bin-GWAS）比基于SNP水平的全基因组关联研究（SNP-GWAS）更具功效。
本研究旨在通过SNP-GWAS和bin-GWAS估计水稻中控制稻米外观品质的QTL的遗传效应，比较它们在QTL定位中的功效，并从4个亲本中鉴定所有检测到的QTL的优良等位基因以进行遗传改良。
在两种环境下种植一个四交MAGIC群体及其4个亲本，以剖析水稻外观品质的遗传基础。同时进行SNP-GWAS和bin-GWAS以进行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。
通过SNP-GWAS和bin-GWAS分别鉴定出16个和20个与稻米外观品质相关的QTL。一个轻微垩白QTL被定位到一个30 kb的基因组区域，其中OsMH_08T0121900是潜在的候选基因，因为其编码的蛋白葡聚糖内切-1,3-β-葡萄糖苷酶前体参与淀粉和蔗糖代谢途径。垩白和透明度的优良亲本等位基因以及两个QTL几乎都由优质亲本Cypress和越晶丝苗（YJSM）携带，而劣质亲本桂朝2号（GC2）总是携带劣等位基因。籽粒形状和垩白性状品质最高的前5个重组自交系均携带优良等位基因的基因组合。
鼓励使用SNP-GWAS和bin-GWAS方法与MAGIC群体联合进行QTL定位。q是一个与垩白密切相关的新候选基因。鉴定出了垩白和透明度的优良等位基因，这些优良等位基因的聚合有助于提高水稻外观品质。
