Development of SNP Markers in Medicago archiducis-nicolai Based on GBS-seq

doi:10.13560/j.cnki.biotech.bull.1985.2021-0906

Abstract

Abstract:

In order to provide theoretical support for evaluating and exploiting the genetic resources in Medicago archiducis-nicolai,the SNPs were developed and the preliminary analysis of genetic diversity was carried out. A total of 80 individuals of M. archiducis-nicolai from 5 populations were selected to conduct GBS-seq and SNP markers were developed by using GATK software,and then preliminary analysis of genetic structure and genetic diversity was conducted. A total of 60.79 Gb sequence data was obtained,and 12 796 SNP sites were retained after screening,and SNP mutation types demonstrated obvious transition bias. The observed heterozygosity（H_o）for different geographic sources of M. archiducis-nicolai population was 0.187 68-0.304 36. The expected heterozygosity（H_e）was 0.201 97-0.364 34. The nucleotide diversity index（Pi）was 0.178 32-0.241 34,the population in Qilian of Qinhai province presented a relatively highest genetic diversity. The results of the genetic structure indicated that 5 populations could be divided into 2 groups,and there was highly significant positive correlation between geographical distance and genetic distance among populations of M. archiducis-nicolai. The SNP markers are suitable for analyzing the genetic diversity of M. archiducis-nicolai.

Key words: Medicago archiducis-nicolai, GBS, SNP, genetic structure, genetic diversity

ZHOU Xiao-nan, XU Jin-qing, LEI Yu-qing, WANG Hai-qing. Development of SNP Markers in Medicago archiducis-nicolai Based on GBS-seq[J]. Biotechnology Bulletin, 2022, 38(4): 303-310.

Figures/Tables 7

References 33

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采样地Location	经度Latitude（E）	纬度Longitude（N）	海拔Altitude/m	样本量Sample size
青海日月山RYS	101°7'11.7″	36°26'50.6″	3 311	16
青海祁连QLCD	100°28'3″	38°03'40″	3 008	16
青海大通DTXR	101°24'24″	37°1'1.7″	2 954	16
青海湟源HY	101°13'9″	36°34'30.3″	2 841	16
青海西宁西山XNXS	101°44'17.5″	36°37'17.5″	2 462	16

采样地Location	经度Latitude（E）	纬度Longitude（N）	海拔Altitude/m	样本量Sample size
青海日月山RYS	101°7'11.7″	36°26'50.6″	3 311	16
青海祁连QLCD	100°28'3″	38°03'40″	3 008	16
青海大通DTXR	101°24'24″	37°1'1.7″	2 954	16
青海湟源HY	101°13'9″	36°34'30.3″	2 841	16
青海西宁西山XNXS	101°44'17.5″	36°37'17.5″	2 462	16

群体名称 Population name	测序片段数 Raw reads	碱基数 Raw bases/Gb	过滤后测序片段数Clean reads	过滤后碱基数Clean bases/Gb	酶捕获率 Enzyme catch ratio/%	测序质量 Sequencing quality Q30/%	GC含量 GC content/%
RYS	4 815 069	0.72	3 856 582	0.58	99.39	93.80	53.23
XNXS	4 360 916	0.65	3 468 857	0.52	98.74	93.13	46.40
HY	6 638 025	0.99	5 456 407	0.82	98.85	93.39	49.90
QLCD	4 800 074	0.71	3 981 534	0.60	99.16	93.07	42.29
DTXR	4 884 748	0.73	4 044 807	0.61	99.46	93.33	51.73

群体名称 Population name	测序片段数 Raw reads	碱基数 Raw bases/Gb	过滤后测序片段数Clean reads	过滤后碱基数Clean bases/Gb	酶捕获率 Enzyme catch ratio/%	测序质量 Sequencing quality Q30/%	GC含量 GC content/%
RYS	4 815 069	0.72	3 856 582	0.58	99.39	93.80	53.23
XNXS	4 360 916	0.65	3 468 857	0.52	98.74	93.13	46.40
HY	6 638 025	0.99	5 456 407	0.82	98.85	93.39	49.90
QLCD	4 800 074	0.71	3 981 534	0.60	99.16	93.07	42.29
DTXR	4 884 748	0.73	4 044 807	0.61	99.46	93.33	51.73

群体 Population	HY	RYS	QLCD	XNXS	DTXR
HY	0.0000	0.0093**	0.0282**	0.0138**	0.0146**
RYS		0.0000	0.0369**	0.0213**	0.0171**
QLCD			0.0000	0.0338**	0.0258**
XNXS				0.0000	0.0215**
DTXR					0.0000