Identification of SSR Loci and Development of Polymorphic Markers in Whole Genome of Oat

doi:10.13560/j.cnki.biotech.bull.1985.2023-0697

Abstract

Abstract:

【Objective】 Due to the limited number of SSR markers developed in oat, it is difficult to meet the needs of functional gene mapping and polymorphism marker development in oat.【Method】 Using the published reference genome, the SSR loci of the whole oat genome were retrieved by TBtools software, and their distribution characteristics were analyzed by Excel and SPSS software.【Result】 The SSR was abundant and varied in oat genome. A total of 828 138 SSR loci were identified in the whole genome, with an average density of 78.16 SSR/Mb and an average distance of 12.90 kb. Single, double and trinucleotide repeat types were dominant. The repetitions of the primitives were mainly 5 and 6, and the A/T, AG/CT and AAC/GTT repetitions were the dominant primitives. The SSR loci of oat genome showed moderate polymorphism, with length ranging from 11 to 1 587 bp. Through the systematic identification and analysis of the whole oat gene SSR locus, 52 pairs of polymorphic primers were developed and validated in the test material.【Conclusion】 The development of SSR primers in the reference genome of “Sanfensan” naked oat is effective and feasible, and can be used for further experimental research.

Key words: oats, skin, SSR markers, primer development, polymorphism

CHEN Kai-ling, WU Tao, XU Yi-qun, GAO Jia, ZHANG Mei-jun, LI Xin, JIA Ju-qing. Identification of SSR Loci and Development of Polymorphic Markers in Whole Genome of Oat[J]. Biotechnology Bulletin, 2024, 40(2): 120-129.

Figures/Tables 9

References 32

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亚组 Subgroup	染色体 Chromosome	染色体大小 Size of chromosome/Mb	SSR数量 Number of SSRs	SSR密度 SSR density/(SSR·Mb^-1)	SSR距离 SSR distance/(kb·SSR^-1)
A	1A	551.55	46 585	84.46	11.84
	2A	462.81	41 810	90.34	11.07
	3A	418.65	34 491	82.39	12.14
	4A	468.67	41 615	88.79	11.26
	5A	489.91	40 918	83.52	11.97
	6A	456.82	40 619	88.92	11.25
	7A	497.83	41 202	82.76	12.08
C	1C	459.16	30 835	67.15	14.89
	2C	574.16	38 944	67.83	14.74
	3C	616.20	49 132	79.73	12.54
	4C	701.82	46 713	66.56	15.02
	5C	601.56	41 519	69.02	14.49
	6C	610.20	45 292	74.22	13.47
	7C	530.95	37 060	69.80	14.33
D	1D	473.71	36 983	78.07	12.80
	2D	532.98	41 375	77.63	12.88
	3D	464.06	33 680	72.58	13.78
	4D	451.84	37 661	83.35	12.00
	5D	500.51	39 941	79.80	12.53
	6D	293.84	22 043	75.02	13.33
	7D	498.92	39 720	79.61	12.56
合计Total		10 656.15	828 138	-	-

亚组 Subgroup	染色体 Chromosome	染色体大小 Size of chromosome/Mb	SSR数量 Number of SSRs	SSR密度 SSR density/(SSR·Mb^-1)	SSR距离 SSR distance/(kb·SSR^-1)
A	1A	551.55	46 585	84.46	11.84
	2A	462.81	41 810	90.34	11.07
	3A	418.65	34 491	82.39	12.14
	4A	468.67	41 615	88.79	11.26
	5A	489.91	40 918	83.52	11.97
	6A	456.82	40 619	88.92	11.25
	7A	497.83	41 202	82.76	12.08
C	1C	459.16	30 835	67.15	14.89
	2C	574.16	38 944	67.83	14.74
	3C	616.20	49 132	79.73	12.54
	4C	701.82	46 713	66.56	15.02
	5C	601.56	41 519	69.02	14.49
	6C	610.20	45 292	74.22	13.47
	7C	530.95	37 060	69.80	14.33
D	1D	473.71	36 983	78.07	12.80
	2D	532.98	41 375	77.63	12.88
	3D	464.06	33 680	72.58	13.78
	4D	451.84	37 661	83.35	12.00
	5D	500.51	39 941	79.80	12.53
	6D	293.84	22 043	75.02	13.33
	7D	498.92	39 720	79.61	12.56
合计Total		10 656.15	828 138	-	-

项目 Item	平均值 Average	标准差 Standard deviation	染色体大小 Size of chromosome	SSR密度 SSR density	SSR距离 SSR distance	SSR数量 Number of SSRs
染色体大小Size of chromosome	507.44	85.19	1
SSR密度SSR density	78.16	7.38	-0.38	1
SSR距离SSR distance	12.90	1.24	0.40	-0.99**	1
SSR数量Number of SSRs	39 435.14	5 945.73	0.81**	0.21	-0.20	1

项目 Item	平均值 Average	标准差 Standard deviation	染色体大小 Size of chromosome	SSR密度 SSR density	SSR距离 SSR distance	SSR数量 Number of SSRs
染色体大小Size of chromosome	507.44	85.19	1
SSR密度SSR density	78.16	7.38	-0.38	1
SSR距离SSR distance	12.90	1.24	0.40	-0.99**	1
SSR数量Number of SSRs	39 435.14	5 945.73	0.81**	0.21	-0.20	1

基因组Genome	亚组Subgroup	染色体长度Chromosome length/Mb	SSR数目Number of SSR	SSR密度SSR density/(SSR·Mb^-1)
Sang	A	3 277.34	242 707	73.99
	C	3 867.70	260 585	67.30
	D	3 125.40	223 135	71.32
三分三	A	3 346.24	287 240	85.88
	C	4 094.05	289 495	70.62
	D	3 215.86	251 403	78.01