Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (11): 2079-2091.doi: 10.3864/j.issn.0578-1752.2024.11.003

• SPECIAL FOCUS: SOYBEAN DISEASE RESISTANCE, YIELD AND QUALITY CORRELATION • Previous Articles     Next Articles

Genome Wide Association Analysis of Soluble Sugar Content in Fresh Seeds of Soybean Landraces

ZHANG YuMei1(), DING WenTao2,3(), LAN XinLong1, LI QingHua4, HU RunFang1, GUO Na2,3, LIN GuoQiang1(), ZHAO JinMing2,3()   

  1. 1 Crop Research Institute, Fujian Academy of Agricultural Sciences/Engineering Research Center for Characteristic Dry Crop Varieties Breeding/Fujian Key Laboratory of Vegetable Genetics and Breeding, Fuzhou 350013
    2 Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing 210014
    3 College of Agriculture, Nanjing Agricultural University/National Innovation Platform for Soybean Breeding and Industry-Education Integration/Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs/National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing 210095
    4 Putian Agricultural Sciences Research Institute, Putian 351106, Fujian
  • Received:2022-11-28 Accepted:2023-01-03 Online:2024-06-01 Published:2024-06-07
  • Contact: LIN GuoQiang, ZHAO JinMing

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Abstract:

【Objective】Soluble sugar content is one of the important quality traits of vegetable soybean. The genetic variation and genetic mechanism of soluble sugar content in fresh soybean seeds were studied to provide a basis for germplasm innovation and quality breeding of vegetable soybean.【Method】Using 133 soybean landraces from the Northeast region, the North region, the Huanghuaihai region and the South region, the soluble sugar content of fresh seeds was determined in the three environments of Lianjiang in spring, Fuqing in spring and autumn, in 2021. In combination with 82 187 high-quality SNP markers, the whole genome association analysis of soluble sugar content was conducted based on the mixed linear model MLM (Q+K), and the SNP loci with significantly related to soluble sugar content were identified. The candidate intervals were selected by the significant SNP loci and the extension of 119.07 kb linkage disequilibrium decay distance at both ends. The candidate genes were predicted according to the annotation and tissue expression information of the genes in the candidate intervals.【Result】The variation range of soluble sugar content in fresh seeds under three environments was 3.37-33.84 mg·g-1, the genetic variation coefficient was 24.59%-32.69%, and the heritability of soluble sugar content was 68.14%. 6, 8 and 22 SNPs were significantly associated with the soluble sugar content of fresh seeds were detected in Lianjiang in spring, Fuqing in spring and autumn, respectively, and phenotypic variation was 12.43%-29.27%. A total of 86 genes were obtained in the candidate regions of 9 significant SNP loci with higher interpretation rate of phenotypic variation, and 9 candidate genes were further screened by gene annotation and tissue expression information. These candidate genes are mainly involved in biological processes such as transcription factors, glycoprotein families and carbohydrate synthesis and transport. Among them, Glyma.01g016500, Glyma.13g042100, Glyma.16g131800 and Glyma.16g155300 were more highly expressed in soybean seeds and pods, which can be used as the most potential candidate genes for soluble sugar in fresh soybean seeds.【Conclusion】Through genome-wide association analysis, 36 SNPs significantly associated with soluble sugar content in fresh seeds were detected, and 9 candidate genes were further screened out, which may be involved in the regulation of soluble sugar content in fresh soybean seeds. Among them, Glyma.01g016500, Glyma.13g042100, Glyma.16g131800 and Glyma.16g155300 can be the key candidate genes for regulating soluble sugar content in fresh soybean seeds.

Key words: soybean, fresh seeds, soluble sugar contents, genome wide association analysis, candidate genes

Table 1

Descriptive statistic, ANOVOA and heritability (h2) of soluble sugar content in fresh seeds of soybean landraces"

环境
Environments		 均值
Mean
(mg·g-1)		 标准差
SD
(mg·g-1)		 最小值
Min.
(mg·g-1)		 最大值
Max.
(mg·g-1)		 变异系数
CV
(%)		 显著性Significance 遗传率
h2
(%)
FG FE FG×E
2021CLJ 8.73 2.850 3.37 19.05 32.69 3.01** 4.38** 7.20** 68.14
2021CFQ 10.74 2.641 5.68 18.79 24.59
2021QFQ 11.19 3.431 4.22 33.84 30.66
平均Mean 10.31 2.161 6.03 22.10 20.96

Fig.1

The frequency distribution and boxplot of basic statistics of soluble sugar content in soybean landraces fresh seeds 2021CLJ: Lianjiang in Spring 2021; 2021CFQ: Fuqing in Spring 2021; 2021QFQ: Fuqing in Autumn 2021. The same as below"

Fig. 2

Manhattan plots and Q-Q plots of GWAS for soluble sugar content in soybean landraces fresh seeds"

Table 2

Significantly associated SNPs of soluble sugar content in soybean landraces fresh seeds"

环境
Environments		 标记
Markers		 染色体
Chromosome		 物理位置
Position (bp)		 等位变异
Allelic		 显著性
-log10(P)		 表型变异解释率
R2 (%)
2021CLJ AX-90503091 1 51857659 G/A 3.53 14.28
AX-90375080 6 4456132 A/G 3.72 15.15
AX-90439820 14 7015035 C/T 3.59 14.64
AX-90326993 16 28742781 T/C 3.66 14.68
AX-90345551 16 28826370 C/T 3.86 15.72
AX-90366289 16 32782857 T/G 3.69 14.92
2021CFQ AX-90498034 3 38220637 G/A 3.71 14.08
AX-90388849 3 38318720 C/A 3.85 14.75
AX-90399131 6 41556768 G/A 3.99 15.32
AX-90305393 6 41636432 T/C 3.65 13.81
AX-90414763 6 41661485 T/C 3.90 15.08
AX-90521281 6 41672853 G/T 3.90 15.08
AX-90430712 6 41739316 G/A 3.56 13.43
AX-90491158 18 833161 A/C 3.79 14.36
2021QFQ AX-90523492 1 1643221 T/C 4.13 19.65
AX-90471910 2 15509622 T/G 3.73 14.71
AX-90463831 5 37457082 G/A 4.33 16.52
AX-90337094 8 18928439 C/G 3.87 13.99
AX-90515230 8 18936718 C/T 4.04 16.18
AX-90318719 8 27518867 T/G 3.52 12.43
AX-90511533 8 34944396 C/T 3.70 13.72
AX-90474383 9 6551732 T/G 3.58 13.30
AX-90385515 9 6624803 A/C 3.51 13.64
AX-90358417 9 6771694 T/A 3.81 13.83
AX-90308466 9 6801826 C/T 3.58 13.28
AX-90423241 9 6931879 T/C 3.57 12.90
AX-90343217 9 6940434 C/T 3.71 13.46
AX-90409115 9 6969624 T/C 3.73 13.94
AX-90407481 10 3759843 G/A 3.82 14.71
AX-90467097 10 41183218 C/T 3.69 14.45
AX-90376167 11 32722314 A/G 3.54 12.78
AX-90350462 13 13577053 A/G 4.35 16.45
AX-90317931 13 18042528 T/G 3.89 13.17
AX-90364912 15 5490816 C/T 3.91 16.89
AX-90351400 16 31631250 C/T 6.81 29.27
AX-90304999 18 46549803 G/A 3.69 13.49

Table 3

Gene information associated with significant markers"

标记
Marker		 物理位置
Position (bp)		 染色体
Chromosome		 等位变异
Allelic		 关联基因
Associated gene		 位置与变异
Region and variant
AX-90523492 1643221 1 T>C Glyma.01g015600 基因下游Downstream
Glyma.01g015800 基因下游Downstream
Glyma.01g015900 基因下游Downstream
Glyma.01g016100 基因下游Downstream
Glyma.01g016500 基因下游Downstream
Glyma.01g016800 基因下游Downstream
Glyma.01g016900 基因下游Downstream
Glyma.01g017000 基因下游Downstream
Glyma.01g017200 外显子，同义突变Exon, synonymous
Glyma.01g017300 基因上游Upstream
Glyma.01g017400 基因上游Upstream
Glyma.01g018300 基因上游Upstream
AX-90375080 4456132 6 A>G Glyma.06g057700 基因下游Downstream
Glyma.06g058000 基因下游Downstream
Glyma.06g058100 基因下游Downstream
Glyma.06g058500 基因下游Downstream
Glyma.06g058600 基因下游Downstream
Glyma.06g059000 内含子突变Intron variant
Glyma.06g059500 基因上游Upstream
Glyma.06g059700 基因上游Upstream
Glyma.06g060200 基因上游Upstream
Glyma.06g060300 基因上游Upstream
AX-90399131 41556768 6 G>A Glyma.06g245400 基因下游Downstream
AX-90414763 90414763 6 T>C Glyma.06g245500 基因下游Downstream
AX-90521281 90521281 6 G>T Glyma.06g245600 基因下游Downstream
Glyma.06g245700 基因下游Downstream
Glyma.06g245800 基因下游Downstream
Glyma.06g245900 基因下游Downstream
Glyma.06g246000 基因下游Downstream
Glyma.06g246100 上游基因突变Upstream gene variant
Glyma.06g246200 基因上游Upstream
Glyma.06g246300 基因上游Upstream
Glyma.06g246400 基因上游Upstream
Glyma.06g246500 基因上游Upstream
Glyma.06g246600 外显子，非同义突变Exon, nonsynonymous
Glyma.06g246800 外显子，同义突变Exon, synonymous
Glyma.06g246900 基因上游Upstream
Glyma.06g247100 基因上游Upstream
Glyma.06g247200 基因上游Upstream
Glyma.06g247300 基因上游Upstream
Glyma.06g247600 基因上游Upstream
AX-90515230 18936718 8 C>T Glyma.08g230100 基因下游Downstream
Glyma.08g230600 基因下游Downstream
Glyma.08g230800 基因下游Downstream
Glyma.08g230900 基因下游Downstream
Glyma.08g231000 内含子突变Intron variant
Glyma.08g231400 基因上游Upstream
Glyma.08g231500 基因上游Upstream
Glyma.08g231600 基因上游Upstream
Glyma.08g231800 基因上游Upstream
AX-90350462 13577053 13 A>G Glyma.13g042100 基因下游Downstream
Glyma.13g042200 基因下游Downstream
Glyma.13g042300 基因下游Downstream
Glyma.13g042600 外显子，同义突变Exon synonymous
Glyma.13g042700 基因上游Upstream
Glyma.13g042800 基因上游Upstream
Glyma.13g042900 基因上游Upstream
Glyma.13g043000 基因上游Upstream
Glyma.13g043500 基因上游Upstream
Glyma.13g043600 基因上游Upstream
AX-90345551 28826370 16 C>T Glyma.16g131800 基因下游Downstream
Glyma.16g131900 基因下游Downstream
Glyma.16g132000 基因下游Downstream
Glyma.16g132100 基因间变异Intergenic region
Glyma.16g132200 基因间变异Intergenic region
Glyma.16g132500 基因上游Upstream
Glyma.16g132600 基因上游Upstream
Glyma.16g132700 基因上游Upstream
Glyma.16g132800 基因上游Upstream
AX-90351400 31631250 16 C>T Glyma.16g155100 基因下游Downstream
Glyma.16g155200 基因下游Downstream
Glyma.16g155300 基因下游Downstream
Glyma.16g155400 基因下游Downstream
Glyma.16g155500 基因下游Downstream
Glyma.16g155600 基因下游Downstream
Glyma.16g155700 基因下游Downstream
Glyma.16g155800 基因下游Downstream
Glyma.16g156100 外显子，非同义突变Exon, nonsynonymous
Glyma.16g156200 基因上游Upstream
Glyma.16g156300 基因上游Upstream
Glyma.16g156400 基因上游Upstream
Glyma.16g156500 基因上游Upstream
Glyma.16g156600 基因上游Upstream
Glyma.16g156700 基因上游Upstream
Glyma.16g156800 基因上游Upstream
Glyma.16g157100 基因上游Upstream

Table 4

Function annotation for candidate genes of soluble sugar content in soybean landraces fresh seeds"

候选基因
Candidate genes		 同源基因
Homologous gene		 功能注释
Function annotation
Glyma.01g016100 AT1G05670.1 PPR超家族蛋白PPR superfamily protein
Glyma.01g016500 AT4G25960.1 P-糖蛋白2 P-glycoprotein 2
Glyma.06g058600 AT5G21280.1 富含羟脯氨酸的糖蛋白Glycoprotein rich in hydroxyproline
Glyma.08g231800 AT1G30320.1 Remorin家族蛋白Remorin family protein
Glyma.13g042100 AT5G53140.1 蛋白磷酸酶2C家族蛋白Protein phosphatase 2C family proteins
Glyma.16g131800 AT4G36360.1 β-半乳糖苷酶3 β-galactosidase 3
Glyma.16g155300 AT3G60530.1 GATA转录因子GATA transcription factors
Glyma.16g156800 AT1G22710.1 蔗糖质子转运体2 Sucrose proton transporter 2
Glyma.16g157100 AT1G71880.1 蔗糖质子转运体1 Sucrose proton transporter 1

Fig. 3

Tissue expression heat map of candidate genes for soluble sugar content in fresh seeds of soybean landraces"

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