大豆抗旱遗传位点及候选基因发掘

doi:10.13304/j.nykjdb.2022.1035

摘要/Abstract

摘要：

叶绿素是植物光合作用必需色素，干旱胁迫可影响其合成并降低光合效率，进而影响大豆产量。为发掘有关大豆干旱胁迫叶绿素含量遗传位点，以199份大豆品种资源构建的自然群体为材料，测定其干旱及正常条件下的叶绿素含量，计算抗旱指数（drought resistance index， DRI），并依据抗旱指数和20×重测序基因型进行全基因组关联分析（genome-wide association study， GWAS）。结果表明，共定位到237个显著关联单核苷酸多态性（single nucleotide polymorphism，SNP）标记（划分为18个位点），分别位于1、2、3、7、10、16、17及18号染色体。在16号染色体关联到181个SNPs，占总SNPs的76.37%，属热点区域，其中9个位于基因内含子区，17个位于外显子区，11个位于上游，10个位于下游，1个位于3’UTR。基于显著关联SNPs获得57个基因，依据基因注释、DNA水平SNP等位变异、RNA水平表达模式，对57个基因进行分析，筛选出3个与大豆抗旱指数相关基因，其中Glyma.16G063600编码F-box蛋白，Glyma.10G007000编码AP2-EREBP转录因子，Glyma.17G143900编码AP2/ERF结构域蛋白。以上研究结果为大豆抗旱育种奠定理论基础。

关键词: 大豆, 叶绿素含量, 干旱胁迫, 全基因组关联分析

Abstract:

Chlorophyll is an essential pigment for plant photosynthesis. Drought tolerance affects chlorophyll synthesis， reduces photosynthetic efficiency， and decreases soybean yield. In order to explore the genetic loci of chlorophyll content in soybean under drought stress， drought resistance index （DRI） were calculated by chlorophyll contents under drought and well-watered conditions. Moreover， based on the DRI and re-sequenced genotypes of the soybean natural population （199 accessions） at 20× sequencing depth， the genome-wide association study （GWAS） was performed. The results showed that 237 single nucleotide polymorphisms（SNPs） in 18 loci on the chromosomes 1， 2， 3， 7， 10， 16， 17 and 18 were identified to associate with DRI. Moreover， 181 SNPs （76.37% of the total） were located on chromosome 16， of which 9 SNPs were located in the gene introns， 17 in exons， 21 in upstream or downstream， and 1 in 3’UTR. Based on these， 57 candidate genes flanking the associated SNPs were found， and according to the gene annotation， SNP mutation， and RNA expression， 3 candidate genes， Glyma.16G063600 （F-box protein）， Glyma.10G007000 （AP2-EREBP）， and Glyma.17G143900 （AP2/ERF） were screened out which might be responsible for the drought tolerance in soybean. Above results provided important theoretical foundation for drought tolerance genetic improvement in soybean.

Key words: soybean, chlorophyll content, drought stress, GWAS

中图分类号:

S565.1

田蕊, 张华, 黄玫红, 邵振启, 李喜焕, 张彩英. 大豆抗旱遗传位点及候选基因发掘[J]. 中国农业科技导报, 2023, 25(9): 69-82.

Rui TIAN, Hua ZHANG, Meihong HUANG, Zhenqi SHAO, Xihuan LI, Caiying ZHANG. Mining of Candidate Genes and Genetic Loci Conferring Drought Tolerance in Soybean[J]. Journal of Agricultural Science and Technology, 2023, 25(9): 69-82.

图/表 14

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位点 Locus	染色体 Chromosome	SNP区间 SNP interval/bp	SNP数目 SNP number	最显著SNP Highest association SNP	-log₁₀（P）	环境 Environment
Locus 1	Chr1	40 004 695～40 004 931	6	Gm01：40004755	6.24	Mean、BLUP、E1、E2、E3
Locus 2	Chr2	687 623～688 028	5	Gm02：687623	5.08	Mean、E1、E2、E3
Locus 3	Chr3	41 106 456	1	Gm03：41106456	5.15	Mean、E1
Locus 4	Chr7	4 696 623	1	Gm07：4696623	5.16	BLUP
Locus 5	Chr10	348 939	1	Gm10：348939	5.16	Mean、BLUP、E1、E2、E3
Locus 6	Chr10	656 486～694 780	5	Gm10：656486	5.57	Mean、BLUP、E1、E2、E3
Locus 7	Chr10	703 703～707 681	15	Gm10：703703	5.42	Mean、E1、E2、E3
Locus 8	Chr10	873 426	1	Gm10：873426	5.07	Mean、E1、E2、E3
Locus 9	Chr10	987 325～1 087 932	5	Gm10：1086041	5.20	Mean、BLUP、E1
Locus 10	Chr16	5 831 709～5 931 196	3	Gm16：5931196	5.38	E1、E2、E3
Locus 11	Chr16	6 226 168～6 321 014	62	Gm16：6302330	5.81	Mean、BLUP、E1、E2、E3
Locus 12	Chr16	6 329 004～6 419 081	83	Gm16：6353406	7.11	Mean、BLUP、E1、E2、E3
Locus 13	Chr16	6 438 949～6 534 022	27	Gm16：6472037	6.23	Mean、BLUP、E1、E2、E3
Locus 14	Chr16	6 564 434～6 651 708	6	Gm16：6564434	5.31	Mean、BLUP、E1、E2、E3
Locus 15	Chr17	11 692 552～11 760 989	9	Gm17：11711567	5.64	Mean、BLUP、E1、E2、E3
Locus 16	Chr18	39 040 317	1	Gm18：39040317	5.85	Mean、E1、E2、E3
Locus 17	scaffold	58 888	1	scaffold_82：58888	6.24	Mean、BLUP、E1、E2、E3
Locus 18	scaffold	14 534～15 780	5	scaffold_288：14774	6.46	Mean、BLUP、E1、E2、E3

位点 Locus	染色体 Chromosome	SNP区间 SNP interval/bp	SNP数目 SNP number	最显著SNP Highest association SNP	-log₁₀（P）	环境 Environment
Locus 1	Chr1	40 004 695～40 004 931	6	Gm01：40004755	6.24	Mean、BLUP、E1、E2、E3
Locus 2	Chr2	687 623～688 028	5	Gm02：687623	5.08	Mean、E1、E2、E3
Locus 3	Chr3	41 106 456	1	Gm03：41106456	5.15	Mean、E1
Locus 4	Chr7	4 696 623	1	Gm07：4696623	5.16	BLUP
Locus 5	Chr10	348 939	1	Gm10：348939	5.16	Mean、BLUP、E1、E2、E3
Locus 6	Chr10	656 486～694 780	5	Gm10：656486	5.57	Mean、BLUP、E1、E2、E3
Locus 7	Chr10	703 703～707 681	15	Gm10：703703	5.42	Mean、E1、E2、E3
Locus 8	Chr10	873 426	1	Gm10：873426	5.07	Mean、E1、E2、E3
Locus 9	Chr10	987 325～1 087 932	5	Gm10：1086041	5.20	Mean、BLUP、E1
Locus 10	Chr16	5 831 709～5 931 196	3	Gm16：5931196	5.38	E1、E2、E3
Locus 11	Chr16	6 226 168～6 321 014	62	Gm16：6302330	5.81	Mean、BLUP、E1、E2、E3
Locus 12	Chr16	6 329 004～6 419 081	83	Gm16：6353406	7.11	Mean、BLUP、E1、E2、E3
Locus 13	Chr16	6 438 949～6 534 022	27	Gm16：6472037	6.23	Mean、BLUP、E1、E2、E3
Locus 14	Chr16	6 564 434～6 651 708	6	Gm16：6564434	5.31	Mean、BLUP、E1、E2、E3
Locus 15	Chr17	11 692 552～11 760 989	9	Gm17：11711567	5.64	Mean、BLUP、E1、E2、E3
Locus 16	Chr18	39 040 317	1	Gm18：39040317	5.85	Mean、E1、E2、E3
Locus 17	scaffold	58 888	1	scaffold_82：58888	6.24	Mean、BLUP、E1、E2、E3
Locus 18	scaffold	14 534～15 780	5	scaffold_288：14774	6.46	Mean、BLUP、E1、E2、E3

SNP	石76368 Shi 76368	沧0719 Cang 0719	冀豆27 Jidou 27	HN0906	石豆5号 Shidou 5	HN1030	邯15-685 Han15-685	冀11B9 Ji 11B9	沧0627 Cang 0627	冀10B5 Ji 10B5
Gm07：4696623	AA	AA	AA	AA	AA	AA	GG	—	GG	GG
Gm10：348939	CC	CC	CC	—	CC	TT	TT	TT	TT	TT
Gm10：656486	AA	AA	AA	AA	AA	TT	TT	TT	TT	TT
Gm10：703703	CC	CC	CC	CC	CC	AA	AA	AA	AA	AA
Gm10：873426	GG	GG	GG	GG	GG	AA	AA	AA	AA	AA
Gm10：1086041	GG	GG	GG	GG	GG	GG	AA	AA	AA	AA
Gm16：6302330	TT	TT	TT	TT	TT	CC	CC	CC	CC	CC
Gm16：6353406	AA	AA	AA	AA	AA	GG	GG	GG	GG	GG
Gm16：6564434	GG	GG	GG	GG	GG	TT	TT	TT	TT	TT
Gm17：11711567	CC	CC	CC	CC	CC	TT	TT	TT	TT	TT
scaffold_288：14774	GG	—	GG	GG	GG	CC	CC	CC	CC	CC
抗旱指数 Drought resistance index	1.07	1.08	1.09	1.11	1.13	1.70	1.71	1.80	1.81	1.83
优异等位变异数量 Number of elite allele	0	0	0	0	0	9	11	10	11	11

SNP	石76368 Shi 76368	沧0719 Cang 0719	冀豆27 Jidou 27	HN0906	石豆5号 Shidou 5	HN1030	邯15-685 Han15-685	冀11B9 Ji 11B9	沧0627 Cang 0627	冀10B5 Ji 10B5
Gm07：4696623	AA	AA	AA	AA	AA	AA	GG	—	GG	GG
Gm10：348939	CC	CC	CC	—	CC	TT	TT	TT	TT	TT
Gm10：656486	AA	AA	AA	AA	AA	TT	TT	TT	TT	TT
Gm10：703703	CC	CC	CC	CC	CC	AA	AA	AA	AA	AA
Gm10：873426	GG	GG	GG	GG	GG	AA	AA	AA	AA	AA
Gm10：1086041	GG	GG	GG	GG	GG	GG	AA	AA	AA	AA
Gm16：6302330	TT	TT	TT	TT	TT	CC	CC	CC	CC	CC
Gm16：6353406	AA	AA	AA	AA	AA	GG	GG	GG	GG	GG
Gm16：6564434	GG	GG	GG	GG	GG	TT	TT	TT	TT	TT
Gm17：11711567	CC	CC	CC	CC	CC	TT	TT	TT	TT	TT
scaffold_288：14774	GG	—	GG	GG	GG	CC	CC	CC	CC	CC
抗旱指数 Drought resistance index	1.07	1.08	1.09	1.11	1.13	1.70	1.71	1.80	1.81	1.83
优异等位变异数量 Number of elite allele	0	0	0	0	0	9	11	10	11	11

基因型Genotype	品种数量Variety number	抗旱指数Drought resistance index
基因型Ⅰ （CCC）Genotype Ⅰ （CCC）	70	0.97 d
基因型Ⅱ （CCT）Genotype Ⅱ （CCT）	36	1.03 c
基因型Ⅲ （CAC）Genotype Ⅲ （CAC）	17	1.10 abc
基因型Ⅳ （CAT）Genotype Ⅳ （CAT）	13	1.14 ab
基因型Ⅴ （ACC）Genotype Ⅴ （ACC）	35	1.03 c
基因型Ⅵ （ACT）Genotype Ⅵ （ACT）	17	1.04 c
基因型Ⅶ （AAT）Genotype Ⅶ （AAT）	7	1.20 a
基因型Ⅷ （AAC）Genotype Ⅷ （AAC）	4	1.18 ab