Development of Functional Markers and Identification of Haplotypes for Rice Grain Width Gene GS5

doi:10.16819/j.1001-7216.2016.6038

Abstract

Abstract:

As a major component of rice grain shape, the grain width is an important trait which is correlated with the rice yield and quality. Based on the alignment of gene GS5 genomic DNA sequence, two functional markers were developed based on two missense polymorphisms (ACC/CTA in the exon2, A/C in the exon9, respectively). Subsequently, the markers were used to identify the genotypes of gene GS5 in the 294 accessions of a rice mini-core collection and 65 japonica varieties released in Jiangsu Province from 2007 to 2013. We found that the allelic variations at the two target loci had significant or extremely significant differences in the grain shape traits(grain length, grain width and ratio of length to width). Based on the two variation sites of gene GS5, four haplotypes (combinations) were found in the rice mini-core collection, and had extremely significant effect on grain width, grain thickness and ratio of length to width in the indica group, and on grain width and ratio of length to width in the japonica group, respectively. While in japonica varieties released by Jiangsu, only two haplotypes, Hap1 (represented by 64 varieties) and Hap2 (represented by one variety) were found. The results will lay a foundation for the application of the useful allelic variations or haplotypes of gene GS5 to the rice yield and quality breeding program.

Key words: rice, grain shape, gene GS5, functional markers, haplotype

摘要：

水稻粒宽是影响籽粒粒形的重要因素之一,也是一个与水稻产量和稻米品质密切相关的重要性状。在基因GS5序列分析的基础上,对该基因第2外显子的ACC/CTA和第9外显子A/C的两个变异位点分别开发了功能标记,并将其用于294份水稻微核心种质和2007-2013年江苏省审定的65份粳稻品种的基因型鉴定。研究结果表明,这两个变异位点的等位变异在水稻籽粒的粒长、粒宽和长宽比性状上存在显著或极显著的差异;其在水稻微核心种质中组成的4种单倍型在水稻籼亚种的粒宽、粒厚和长宽比性状上存在极显著的差异,在粳亚种的粒宽和长宽比性状上存在极显著的差异;而江苏省审定的粳稻品种中仅发现Hap1和Hap2两种单倍型,其分别有64个和1个代表性品种。这些研究结果为水稻产量和稻米品质育种中充分利用GS5的优异等位基因或单倍型奠定了基础。

关键词: 水稻, 粒形, 基因GS5, 功能标记, 单倍型

CLC Number:

Chuan-deng YI, De-rong WANG, Wei JIANG, Wei LI, Xiao-jun CHENG, Ying WANG, Yong ZHOU, Guo-hua LIANG, Ming-hong GU. Development of Functional Markers and Identification of Haplotypes for Rice Grain Width Gene GS5[J]. Chinese Journal OF Rice Science, 2016, 30(5): 487-492.

裔传灯, 王德荣, 蒋伟, 李玮, 成晓俊, 王颖, 周勇, 梁国华, 顾铭洪. 水稻粒宽基因GS5的功能标记开发和单倍型鉴定[J]. 中国水稻科学, 2016, 30(5): 487-492.

Figures/Tables 5

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标记名称 Marker	变异位点所在区域^a Region of sequence variation^a	基因型 Genotype	引物序列 Primer sequence	标记类型 Marker type
GS5-1	Exon 2(817 bp)	ACC/CTA	F:GCAAGACAAGGAGCAGCACTA	CAPS-DdeⅠ
			R:AGAAGCCGACCCCAACAG
GS5-2	Exon 9(3796 bp)	A/C	F:CAGTTCTCGGTACTGCGTCGA	dCAPS-SalⅠ
			R:CACAAACCTCCCAGCAACC

标记名称 Marker	变异位点所在区域^a Region of sequence variation^a	基因型 Genotype	引物序列 Primer sequence	标记类型 Marker type
GS5-1	Exon 2(817 bp)	ACC/CTA	F:GCAAGACAAGGAGCAGCACTA	CAPS-DdeⅠ
			R:AGAAGCCGACCCCAACAG
GS5-2	Exon 9(3796 bp)	A/C	F:CAGTTCTCGGTACTGCGTCGA	dCAPS-SalⅠ
			R:CACAAACCTCCCAGCAACC

性状 Trait	GS5-1				GS5-2
性状 Trait	基因型 Genotype	样本数 Sample number	平均数± 标准误 Mean±SE	t值 t value	基因型 Genotype	样本数 Sample number	平均数± 标准误 Mean±SE	t值 t value
粒长 Grain length/mm	ACC	170	8.03±0.08	2.98^**	A	210	8.09±0.07	2.33^*
	CTA	124	8.34±0.07		C	83	8.33±0.08
粒宽 Grain width/mm	ACC	170	3.05±0.03	2.21^*	A	210	3.04±0.03	2.01^*
	CTA	124	2.97±0.02		C	83	2.96±0.03
粒厚 Grain thickness/mm	ACC	170	2.13±0.01	1.03	A	210	2.13±0.01	1.68
	CTA	124	2.11±0.01		C	83	2.10±0.01
长宽比 Ratio of length to width	ACC	170	2.70±0.05	2.29^*	A	210	2.72±0.04	2.04^*
	CTA	124	2.84±0.04		C	83	2.85±0.05
千粒重 1000-grain weight/g	ACC	170	24.71±0.31	0.26	A	210	24.74±0.28	0.04
	CTA	124	24.82±0.30		C	83	24.75±0.33

性状 Trait	GS5-1				GS5-2
性状 Trait	基因型 Genotype	样本数 Sample number	平均数± 标准误 Mean±SE	t值 t value	基因型 Genotype	样本数 Sample number	平均数± 标准误 Mean±SE	t值 t value
粒长 Grain length/mm	ACC	170	8.03±0.08	2.98^**	A	210	8.09±0.07	2.33^*
	CTA	124	8.34±0.07		C	83	8.33±0.08
粒宽 Grain width/mm	ACC	170	3.05±0.03	2.21^*	A	210	3.04±0.03	2.01^*
	CTA	124	2.97±0.02		C	83	2.96±0.03
粒厚 Grain thickness/mm	ACC	170	2.13±0.01	1.03	A	210	2.13±0.01	1.68
	CTA	124	2.11±0.01		C	83	2.10±0.01
长宽比 Ratio of length to width	ACC	170	2.70±0.05	2.29^*	A	210	2.72±0.04	2.04^*
	CTA	124	2.84±0.04		C	83	2.85±0.05
千粒重 1000-grain weight/g	ACC	170	24.71±0.31	0.26	A	210	24.74±0.28	0.04
	CTA	124	24.82±0.30		C	83	24.75±0.33

籽粒性状与变异来源 Grain trait and source of variation	籼亚种 indica			粳亚种 japonica
籽粒性状与变异来源 Grain trait and source of variation	自由度 df	平方和 Mean square	F值 F value	自由度 df	平方和 Mean square	F值 F value
粒长Grain length
单倍型间Among haplotypes	3	0.929	1.272	3	2.482	3.493^*
单倍型内Within haplotypes	154	0.730		132	0.711
粒宽 Grain width
单倍型间Among haplotypes	3	0.568	6.131^**	3	0.377	3.940^**
单倍型内Within haplotypes	154	0.093		132	0.096
粒厚 Grain thickness
单倍型间Among haplotypes	3	0.129	7.354^**	3	0.038	1.305
单倍型内Within haplotypes	154	0.018		132	0.029
长宽比 Ratio of length to width
单倍型间 Among haplotypes	3	1.424	5.145^**	3	0.973	5.141^**
单倍型内 Within haplotypes	154	0.277		132	0.189
千粒重 1000-grain weight
单倍型间Among haplotypes	3	31.593	2.470	3	4.165	0.279
单倍型内Within haplotypes	154	12.788		132	14.953