Introduction

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).

Objectives

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.

Methods

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.

Results

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.

Conclusions

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.

中文翻译：

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基于 bin 的全基因组关联研究揭示了在水稻中使用 4 向 MAGIC 种群改善外观质量的优越等位基因

介绍

多亲群体为我们提供了识别控制遗传改良性状的优良等位基因的机会。bin 水平的全基因组关联研究 (bin-GWAS) 在 QTL 作图中的能力预计比 SNP 水平的 GWAS (SNP-GWAS) 更强。

目标

本研究旨在通过 SNP-GWAS 和 bin-GWAS 评估 QTL 赋予水稻籽粒外观品质的遗传效应，比较它们在 QTL 作图中的能力，并确定来自 4 个亲本的所有检测到的 QTL 的优良等位基因，用于遗传改良。

方法

在两个环境中培养了一个4-way MAGIC群体及其四个创始人，以剖析水稻籽粒外观品质的遗传基础。SNP-GWAS 和 bin-GWAS 均用于 QTL 作图。4个亲本箱/等位基因之间的多重比较用于鉴定优越等位基因。

结果

通过 SNP-GWAS 和 bin-GWAS 分别鉴定了 16 个和 20 个与谷物外观质量相关的 QTL。一个小的白垩质 QTL qPGWC8.2/qDEC8被分配到一个 30-kb 的基因组区域，其中 OsMH_08T0121900 是潜在的候选基因，因为它的编码蛋白葡聚糖内 1,3-β-葡萄糖苷酶前体参与淀粉和蔗糖代谢途径。GS3、GL3.1、GW5、GW7和Chalk5的优良亲本等位基因优质亲本Cypress和越景思妙(YJSM)几乎都携带了两个QTL，而劣质亲本贵巢2号(GC2)则始终携带劣等位基因。粒形和垩白性状质量最高的前5个重组自交系均携带优良等位基因的基因组合。

结论

鼓励使用 SNP 和 bin-GWAS 方法与 MAGIC 群体进行联合 QTL 作图。q PGWC8.2/qDEC8是一种与白垩密切相关的新型候选基因。鉴定了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金字塔化有助于提高水稻外观品质。