利用PyBSASeq算法挖掘大豆百粒重相关位点与候选基因

doi:10.3724/SP.J.1006.2022.14008

Abstract

Abstract:

The PyBSASeq algorithm, based on quantifying the enrichment of likely trait-associated SNPs in a chromosomal interval, was proved more suitable for genetic analysis of complex quantitative traits in bulked segregant analysis. In this study, to identify the loci and candidate genes of 100-seed weight (SW) in soybean using the PyBSASeq algorithm, 149 RILs derived from the hybrid of ‘Huapidou’ and ‘Qihuang 26’ were used as materials. As a result, 11 candidate regions closely associated with SW were identified by mining the 100-grain weight related loci of soybean, which were located on chromosomes 1, 2, 4, 7, 9, 14, and 16, respectively. Among these regions, qSW4-1, qSW9-1, qSW9-2, and qSW7-1 were consistent with the QTLs for 100-seed weight reported previously, and a total of 218 coding genes were included in the candidate regions. Among these genes, Glyma.02G075000 and Glyma.04G082500 were predicted to be candidate genes using gene expressional and haplotype analysis. Bioinformatics analysis showed that the candidate genes were mainly involved in sugar transport and biosynthesis of Vitamin E. The results will be helpful to elucidate the genetic mechanism of seed weight regulation in soybean and provide a reference for the study of quantitative trait based on BSA-Seq method.

Key words: soybean, 100-seed weight, PyBSASeq, SLAF-Seq

WANG Juan, ZHANG Yan-Wei, JIAO Zhu-Jin, LIU Pan-Pan, CHANG Wei. Identification of QTLs and candidate genes for 100-seed weight trait using PyBSASeq algorithm in soybean[J].Acta Agronomica Sinica, 2022, 48(3): 635-643.

Figures/Tables 7

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染色体 Chromosome	QTL数量 Numbers of QTLs	SNP总数 Total number of SNP	QTL/SNP (%)	P值范围 Range of P-value
1	9	57	15.79	1.16×10^-4-6.71×10^-3
2	7	408	1.72	3.07×10^-3-5.99×10^-3
4	33	233	14.16	1.57×10^-3-9.36×10^-3
7	41	163	25.15	9.51×10^-4-8.03×10^-3
9	8	136	5.88	1.45×10^-3-8.13×10^-3
14	73	170	42.94	9.29×10^-5-8.74×10^-3
16	10	239	4.18	6.71×10^-4-8.46×10^-3
总数Total	181	5110	3.54	9.29×10^-5-9.36×10^-3

QTL	染色体 Chromosome	置信区间 Confidence interval (bp)	N_s/N_t	阈值 Threshold	标记/位置 Marker/position	P值 P-value
qSW1-1	1	3353593-4295069	0.80	0.20	Marker4145223/4003887	1.16×10^-3
qSW2-1	2	6277409-6795574	0.46	0.15	Marker6292178/6353955	3.07×10^-3
qSW4-1^[39,40]	4	6745068-7489088	0.84	0.13	Marker6412385/6990477	1.57×10^-3
qSW7-1^[41,42,43]	7	7022337-13703737	1.00	0.33	Marker5915595/8069918	9.51×10^-4
qSW7-2	7	36784876-38304878	1.00	0.10	Marker5871955/37004467	1.82×10^-3
qSW9-1^[13]	9	13567640-13932246	0.67	0.33	Marker4706727/13932246	1.45×10^-3
qSW9-2^[44,45,46]	9	44196936-44232803	0.60	0.20	Marker4584679/44196936	2.06×10^-3
qSW9-3	9	47099980-47940126	1.00	0.33	Marker4755711/47109866	3.11×10^-3
qSW14-1	14	8672359-12688053	1.00	0.09	Marker5172395/11147027	2.93×10^-4
qSW14-2	14	41729998-42423216	1.00	0.13	Marker5029131/41946443	9.29×10^-5
qSW16-1	16	33408123-35629720	0.83	0.17	Marker3332493/33871753	6.71×10^-4

QTL	基因 Gene	位置 Position	功能注释 Annotation
qSW2-1	Glyma.02G073200	Chr02:6399972..6405250	α-1,4-岩藻糖基转移酶 Alpha-1,4-fucosyltransferase
qSW2-1	Glyma.02G075000	Chr02:6535991..6539362	蔗糖转运蛋白(SUT1) Sugar transport protein (SUT1)
qSW4-1	Glyma.04G082300	Chr04:6945685..6946469	维生素E生物合成(生育酚环化酶)Vitamin E biosynthesis (tocopherols)
qSW4-1	Glyma.04G082500	Chr04:6948445..6954177	维生素E生物合成(生育酚环化酶)Vitamin E biosynthesis (tocopherols)
qSW7-2	Glyma.07G200700	Chr07:36897410..36898244	HSP20家族蛋白 HSP20 family protein
qSW9-2	Glyma.09G249500	Chr09:47056885..47062577	羧肽酶C Carboxypeptidase C
qSW14-1	Glyma.14G101900	Chr14:10079123..10080100	ncRNA
qSW14-2	Glyma.14G170900	Chr14:42298358..42306613	β-D-木糖苷酶7相关 β-D-xylosidase 7-related
qSW16-1	Glyma.16G176000	Chr16:33732712..33735090	葡萄糖基/葡萄糖醛基转移酶Glucosyl/glucuronosyl transferases

Identification of QTLs and candidate genes for 100-seed weight trait using PyBSASeq algorithm in soybean

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