Discovering of Candidate Genes for Wheat SDS-Sedimentation Value Using Association Study and Development of KASP Marker

doi:10.13304/j.nykjdb.2024.0895

Abstract

Abstract:

SDS sedimentation value is an important indicator for wheat quality breeding. In this study， genome-wide association study （GWAS） on SDS-sedimentation value was performed in 145 wheat accessions. The results revealed that a cluster of significant signals was identified at the end of 3DL， and combined with the position of the peak SNP and the distance of LD decay， the candidate interval 587.514~589.514 Mb was further determined. Then， variation sites of candidate genes within this region were explored based on the resequencing data （http：//wheat.cau.edu.cn/WheatUnion/）， and candidate gene association study （CGAS） was conducted in combination with SDS-sedimentation value. By integrating association results， gene annotation and gene expression analysis， TraesCS3D03G1092400 was identified as the SDS-sedimentation value-related candidate gene， and was tentatively named TaAGAP-3D. Additionally， a KASP marker Sv-3D-KASP for breeding was developed based on the polymorphic SNP of this gene， and found that TaAGAP-3D（C） was a favorable allele for SDS-sedimentation value. Altogether， these findings provide an effective molecular marker for the genetic improvement of SDS-sedimentation value in wheat， and also provide a reference for further cloning of quality genes.

Key words: common wheat, SDS-sedimentation value, genome-wide association study, candidate gene association study, KASP marker

摘要：

SDS沉降值是小麦品质育种的一项重要指标。对145份小麦品种的SDS沉降值进行了全基因组关联分析，在染色体3DL末端鉴定到成簇的显著信号，结合peak SNP的位置与LD衰减距离锁定587.514~589.514 Mb为候选区段；利用重测序数据（http：//wheat.cau.edu.cn/WheatUnion/）发掘该区段内候选基因的变异位点，再对SDS沉降值的候选基因进行关联分析。综合关联结果、基因注释和基因表达分析，获得沉降值相关候选基因TraesCS3D03G1092400，命名为TaAGAP-3D。基于该基因的多态性SNP位点开发了可供育种利用的KASP标记Sv-3D-KASP，发现TaAGAP-3D（C）为SDS沉降值相关的优异等位变异。研究结果将为小麦SDS沉降值的遗传改良提供有效分子标记，同时也为进一步克隆品质基因提供参考。

关键词: 小麦, SDS沉降值, 全基因组关联分析, 候选基因关联分析, KASP标记

CLC Number:

S511

Haixia LIU, Yinhui ZHANG, Lei ZHUANG, Mengjiao GUO, Li ZHAO, Meijuan WU, Jian HOU, Tian LI, Hongxia LIU, Xueyong ZHANG, Chenyang HAO. Discovering of Candidate Genes for Wheat SDS-Sedimentation Value Using Association Study and Development of KASP Marker[J]. Journal of Agricultural Science and Technology, 2024, 26(12): 18-29.

刘海霞, 张寅辉, 庄蕾, 郭梦娇, 赵李, 吴美娟, 侯健, 李甜, 刘红霞, 张学勇, 郝晨阳. 基于关联分析挖掘小麦SDS沉降值相关候选基因及KASP标记开发[J]. 中国农业科技导报, 2024, 26(12): 18-29.

Figures/Tables 10

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标记 Marker	引物 Primer	引物序列 Primer sequence（5'-3'）
Sv-3D-KASP	F1-FAM （1）： Allele-T	GAAGGTGACCAAGTTCATGCTCGGGTATCGATAGCAGAAGTCTTT
	F2-HEX （2）： Allele-C	GAAGGTCGGAGTCAACGGATTCGGGTATCGATAGCAGAAGTCTTC
	Common-primer-R （3）	TGACACTCCAGATCCCCTTTTT
Sv-3D-dCAPS	dCAPS-F1 （1）	GATGGCACTGTCCCTTGG
	dCAPS-R1 （2）	GGTAGAGTTTGTTGGATTGATT
	dCAPS-F2 （3）	ATCGGGTATCGATAGCAGAAGTCGA
	dCAPS-R2 （4）	GTCAAGCGACCCTTATGTTAT

标记 Marker	引物 Primer	引物序列 Primer sequence（5'-3'）
Sv-3D-KASP	F1-FAM （1）： Allele-T	GAAGGTGACCAAGTTCATGCTCGGGTATCGATAGCAGAAGTCTTT
	F2-HEX （2）： Allele-C	GAAGGTCGGAGTCAACGGATTCGGGTATCGATAGCAGAAGTCTTC
	Common-primer-R （3）	TGACACTCCAGATCCCCTTTTT
Sv-3D-dCAPS	dCAPS-F1 （1）	GATGGCACTGTCCCTTGG
	dCAPS-R1 （2）	GGTAGAGTTTGTTGGATTGATT
	dCAPS-F2 （3）	ATCGGGTATCGATAGCAGAAGTCGA
	dCAPS-R2 （4）	GTCAAGCGACCCTTATGTTAT

环境Environment	均值±标准差Mean±SD/mL	最小值 Min/mL	最大值 Max/mL	变异系数 CV/%	峰度 Kurtosis	偏度 Skewness	广义遗传力H² /%
E1	18.44±2.98	11.30	25.40	16.16	-0.08	0.10	94.10
E2	20.81±3.62	12.10	29.00	17.38	-0.30	0.18
E3	20.40±3.11	12.50	28.50	15.25	-0.41	-0.02
E4	22.74±4.39	13.00	34.10	19.30	-0.25	0.29
E5	20.74±3.88	11.00	30.10	18.72	-0.28	0.27
E6	19.80±3.21	13.00	27.10	16.19	-0.42	0.04
E7	20.65±3.43	11.00	29.90	16.62	-0.21	0.01
BLUP	20.20±2.86	12.64	26.08	14.15	-0.42	-0.05

环境Environment	均值±标准差Mean±SD/mL	最小值 Min/mL	最大值 Max/mL	变异系数 CV/%	峰度 Kurtosis	偏度 Skewness	广义遗传力H² /%
E1	18.44±2.98	11.30	25.40	16.16	-0.08	0.10	94.10
E2	20.81±3.62	12.10	29.00	17.38	-0.30	0.18
E3	20.40±3.11	12.50	28.50	15.25	-0.41	-0.02
E4	22.74±4.39	13.00	34.10	19.30	-0.25	0.29
E5	20.74±3.88	11.00	30.10	18.72	-0.28	0.27
E6	19.80±3.21	13.00	27.10	16.19	-0.42	0.04
E7	20.65±3.43	11.00	29.90	16.62	-0.21	0.01
BLUP	20.20±2.86	12.64	26.08	14.15	-0.42	-0.05

位置 Position/bp	P值 P value	变异类型 Variant type	基因ID Gene ID	参考碱基 REF SNP	突变碱基 ALT SNP	基因注释 Gene annotation
589 508 971	9.51，6.23，6.19，4.52	外显子 Exonic	TraesCS3D03G1092400	C	T	ARF-GTP 酶激活蛋白Arf GTPase activating protein
588 739 600	4.96	上游 Upstream	TraesCS3D03G1089600	C	T	绒毛蛋白Villin
588 637 344	4.78	上游 Upstream	TraesCS3D03G1089400	T	G	羟基肉桂酰-CoA莽草酸/奎宁酸羟基肉桂酰转移酶 Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase
588 246 926	4.61	内含子 Intronic	TraesCS3D03G1088500	A	G	非特异性丝氨酸/苏氨酸蛋白激酶 Non-specific serine/threonine protein kinase
588 516 258	4.37	内含子 Intronic	TraesCS3D03G1089000	T	G	羧基末端肽酶carboxyl-terminal peptidase
588 659 614	4.07	5’-UTR	TraesCS3D03G1089500	G	T	葡萄糖醛酸氧酶4-O-甲基转移酶 Glucuronoxylan 4-O-methyltransferase