QTL-Seq Mapping of Head Rice Rate QTLs in japonica Rice

doi:10.16819/j.1001-7216.2021.201105

Abstract

Abstract:

【Objective】 Rice milling quality is largely measured by head rice rate. So QTL mapping for head rice rate will lay a theoretical basis for rice quality improvement.【Method】 Using an F₂ segregated population from two japonica rice cultivars with similar grain shape but different head rice rates, QTL-Seq bulked segregated sequencing method was used to locate the QTLs controlling head rice rate in japonica rice. 【Result】 Three QTLs were found on chromosomes 8 and 12 by QTL-Seq analysis, and the target regions were further verified by traditional QTL mapping method using 200 F₂ individuals. Of the three QTLs, qHRR8.1 was located at 21.8-23.2 Mb with 10.80% phenotype variation contribution. The QTL qHRR8.2, located on chromosome 8 at 24.2-25.2 Mb and qHRR12, located on chromosome 12 at 2.9-4.5 Mb had smaller contribution of 3.26% and 4.06%, respectively. 【Conclusion】 The head rice rate controlling QTL qHRR8.1 was mapped on chromosome 8, which lay a theoretical foundation for further clone of head rice rate genes, and grain quality improvement in japonica rice.

Key words: rice, grain milling quality, head rice rate, QTL mapping

摘要：

【目的】稻米整精米率是加工品质的重要评价指标之一,其QTL定位将为提升稻米品质提供理论依据。【方法】通过两个粒型相近、整精米率差异极大的粳稻材料构建的F₂分离群体为材料,利用QTL-Seq方法对分离群体中的高整精米率单株和低整精米率单株进行混池重测序以定位粳稻整精米率QTL位点。【结果】经过QTL-Seq分析发现在第8和第12染色体区间存在控制粳稻整精米率的QTL位点。进一步通过200个F₂分离群体单株对第8和12染色体进行InDel分子标记QTL作图,发现粳稻中控制整精米率的QTL位点：qHRR8.1、qHRR8.2和qHRR12。其中,位于第8染色体21.8-23.2 Mb的qHRR8.1表型贡献率达到10.80%,其他两个QTL的贡献率较小。qHRR8.2位于第8染色体24.2-25.2 Mb,表型贡献率为3.26%。位于第12染色体的2.9-4.5 Mb的qHRR12表型贡献率为4.06%。【结论】本研究定位了1个控制粳稻整精米率的主效QTL位点qHRR8.1,对克隆粳稻整精米率控制基因以及在品质育种中提高粳稻整精米率有一定的参考价值。

关键词: 水稻, 稻米加工品质, 整精米率, QTL定位

Xina CHEN, Zeke YUAN, Zhenzhen HU, Quanzhi ZHAO, Hongzheng SUN. QTL-Seq Mapping of Head Rice Rate QTLs in japonica Rice[J]. Chinese Journal OF Rice Science, 2021, 35(5): 449-454.

陈喜娜, 袁泽科, 胡珍珍, 赵全志, 孙红正. 利用QTL-Seq定位粳稻整精米率QTL[J]. 中国水稻科学, 2021, 35(5): 449-454.

Figures/Tables 6

Fig. 1. Phenotype of head rice rates of parents(A) and histogram distribution of the F2 population(B).

Table 1 Head rice rate QTLs detected by QTL-Seq.

染色体 Chromosome	起始 Start / Mb	终止 End / Mb	ΔSNP峰值 ΔSNP peak value	ΔSNP峰值位置 ΔSNP peak position / Mb	G′峰值 G′ peak value	G′峰值位点 G′ peak position / Mb
8	20.3	22.2	-0.27	20.9	8.32	20.9
8	25.9	28.4	-0.28	28.4	10.73	27.5
12	3.2	5.8	-0.29	3.9	14.81	3.9

Fig. 2. Results of the QTL-seq analysis. The gray line indicates the 95% confidence interval. The horizontal axis indicates the genomic position (Mb) and the vertical axis the ED value.

Fig. 3. SNP-index of all the polymorphic sites on 12 chromosomes with sequencing depth greater than 50. Blue dots indicate SNP-index in the mixed pool consisting of plants with high head rice rate, and green dots indicate SNP-index in the mixed pool consisting of plants with low head rice rate. The vertical axis indicates SNP-index and the horizontal axis indicates genomic position (Mb).

Table 2 Head rice rate QTL located on chromosomes 8 and 12.

染色体 Chromosome	名称 Name	位置 Position	左标记 Left marker/Mb	右标记 Right marker/Mb	LOD值 LOD value	表型贡献率 PVE/%
8	qHRR8.1	147.8	21.8	23.2	5.11	10.80
8	qHRR8.2	189.8	24.2	25.2	2.15	3.26
12	qHRR12	7.9	2.9	4.5	2.61	4.06

Fig. 4. Results of head rice rate QTL mapping on chromosomes 8 and 12.

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