适于陆地棉品种身份鉴定的SNP核心位点筛选与评价

doi:10.3724/SP.J.1006.2018.01631

Abstract

Abstract:

Utilizing the genome-wide SNP information to screen the core SNP loci may provide an accurate and efficient method for the identification of upland cotton varieties. Using the CottonSNP80K array, SNP genotyping was performed within 326 upland cotton accessions. Then, the SNP loci were annotated with TM-1 genomic sequence of Gossypium hirsutum (AD₁) genome NBI v1.1 Upland cotton of Nanjing Agricultural University as reference sequence. Statistical analysis of all loci in CottonSNP80K showed that the call rate of 93.85% loci (72 990 in 77 774) was more than 99%, and 61 595 (79.20%) SNPs were polymorphic loci among the tested upland cotton accessions. Among them, minor allele frequency (MAF) of 76.32% (47 009) loci was greater than 0.1. Based on call frequency for each locus > 0.99; loci with polymorphism; MAF > 0.2; heterozygosity rate < 0.05; SNP density with ~400 kb/SNP in each chromosome, we obtained 4857 high-quality core SNP loci. The characteristic statistics of the core SNP loci combination showed that the average call rate was nearly 100%; the average MAF was 0.34; and the average heterozygosity was 0.02. Using these core SNPs, more than 99% of the materials could be identified accurately and effectively. In addition, the identification results of core SNP loci showed extremely significant linear correlation with that of CottonSNP80K. Taken together, a core combination containing 4857 SNP loci for fingerprint identification of upland cotton varieties is constructed, which can accurately identify the purity and reality of modern upland cotton varieties.

Key words: DNA array, fingerprint, SNP, core loci, Upland cotton

Guo-Zhong ZHU,Fang ZHANG,Jie FU,Le-Chen LI,Er-Li NIU,Wang-Zhen GUO. Genome-wide Screening and Evaluation of SNP Core Loci for Identification of Upland Cotton Varieties[J].Acta Agronomica Sinica, 2018, 44(11): 1631-1639.

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染色体 Chr.	染色体长度 Chr. length (Mb)	标记数Number of SNPs	分布密度 Density (kb/SNP)	染色体 Chr.	染色体长度 Chr. length (Mb)	标记数Number of SNPs	分布密度 Density (kb/SNP)
A01	99.9	250	399.5	D01	61.5	153	401.7
A02	83.4	207	403.1	D02	67.3	169	398.1
A03	100.3	248	404.3	D03	46.7	118	395.7
A04	62.9	156	403.3	D04	51.5	128	402.0
A05	92.0	237	388.4	D05	61.9	156	397.0
A06	103.2	255	404.6	D06	64.3	164	392.0
A07	78.3	197	397.2	D07	55.3	138	400.8
A08	103.6	258	401.7	D08	65.9	164	401.8
A09	75.0	183	409.8	D09	51.0	128	398.4
A10	100.9	256	394.0	D10	63.4	156	406.2
A11	93.3	242	385.6	D11	66.1	169	391.1
A12	87.5	215	406.9	D12	59.1	150	394.1
A13	80.0	204	392.0	D13	60.5	156	388.0
Total	1160.2	2908	399.0	Total	774.4	1949	397.3

类型 Type	最大值 Max.	最小值 Min.	平均值 Mean
检出率 Call frequency	1.00	0.99	1.00
最小等位基因频率 MAF	0.50	0.20	0.34
杂合率 Heterozygosity	0.05	0.00	0.02
多态信息含量 PIC	0.50	0.32	0.44

材料 Accession	多态位点(总位点/核心位点) No. of polymorphic loci (total loci/core loci)	多态率(总位点/核心位点) Polymorphic rate (total loci/core loci)
新乡小吉和新乡小吉无绒无絮突变体 Xinxiangxiaoji linted-fuzzless vs. Xinxiangxiaoji lintless-fuzzless	12529/1215	0.161/0.250
徐州142和徐州142无绒无絮突变体 Xuzhou-142 vs. Xuzhou-142 lintless-fuzzless	14808/1488	0.190/0.306
7235和7235纤维突变体 7235 vs. 7235 mutant	19451/2546	0.250/0.524
TM-1和SL1-7-1突变体 TM-1 vs. SL1-7-1	20859/2188	0.268/0.450
TM-1和 MD-17突变体 TM-1 vs. MD-17	23814/2367	0.306/0.487
TM-1和显性光子N1突变体 TM-1 vs. N1 (dominant naked seed)	17678/2170	0.227/0.447
TM-1和隐性光子n2突变体 TM-1 vs. n2 (recessive naked seed)	19996/2446	0.257/0.503
TM-1和im突变体 TM-1 vs. im (immature fiber)	16333/3116	0.210/0.642

SNP	染色体 Chr.	位置 Position (bp)	验证不一致数目 Number of mismatches	引物 Primer (5'-3')
TM3086	A01	86363489	1	F: CTTGATTTTCAATTCAACCAAAAAACTCCG
TM3086	A01	86363489	1	R: AAAATACATGGACGCAACTATCTGATGCATAATTT
TM4824	A02	45647806	0	F: TTGAATGAGTCTCATTTTATCAATTGACCTTTATTA
TM4824	A02	45647806	0	R: TCATAAGGTAATTTGGCAAGTAATTTTGAAAAAGTC
TM7830	A03	89740533	1	F: AAGCCTATATTTTGCCAACTTACCTTGTGCAG
TM7830	A03	89740533	1	R: ATTAAGTTAAAAAGTGCCACATGTCACAAAACCAT
TM9574	A04	51844539	0	F: GGCCCTAATCTTAGGCATAGTTTACCCCAAATAA
TM9574	A04	51844539	0	R: CTTAGGGTAGACGGATGGAGGGATGAGA
TM19508	A07	21138995	0	F: TGCGAGGGATTAAGTTTAGCTTGGAAAGC
TM19508	A07	21138995	0	R: CCATTAGTTGACAATCTTCAAGAACCTTACGAAAA
TM27528	A08	63064554	0	F: GCTCCCATAATTTTCTTTCACTTCGAGACG
TM27528	A08	63064554	0	R: AAGAGAAAGGTGAAAATTTTAAGTACAAAAGGTTGA
TM27748	A08	65768181	0	F: GGCTTTTACTGATTTACATTTTGAACAATGTTAAAG
TM27748	A08	65768181	0	R: GGCTGAATGCTCCTTTACCTTATTTATGGGTT
TM33913	A10	4141534	2	F: GCTCCCTTAAACCCGCAACCTTAGTCA
TM33913	A10	4141534	2	R: AGAAAGTTGTTTCGGCTGGTATTTTGAGGTT
TM53506	D03	2560865	0	F: ATATTTTCTTTTTCTTTTTTCGATAAGATAGAGCAA
TM53506	D03	2560865	0	R: CCAAGGTTAGTTAACTAGAAAAACTGACCGAATCAA
TM58088	D05	33818451	0	F: CTCGTATGTCACAAGACCATCAAAATTTAAATGAA
TM58088	D05	33818451	0	R: TGTATCCCCATTTTGAACACCCACATG
TM69807	D08	63425972	0	F: TTTGTCAATTCTTACCAATTATACCTTCCTACCAAG
TM69807	D08	63425972	0	R: TATGTTTTGAAAATGCAACACCTATAGAAAAAGCAA
TM72841	D09	47573336	0	F: CAGGAATCATTGGGGTTGGACAAGC
TM72841	D09	47573336	0	R: TATGCTTGACTAAGGGATGCATTATCATACATTGTT
TM75830	D11	13710651	0	F: CGCGTCGTAATCGAGTTTCACCGA
TM75830	D11	13710651	0	R: GGTGTCCGGTCCGGTGTGCTTA
TM80004	D13	163793	0	F: GTGGCCACTGAAGAGCAAGCTTAATGA
TM80004	D13	163793	0	R: ATGCATGTTCAAGCTTCTTGGTAATGTCATAATC

Genome-wide Screening and Evaluation of SNP Core Loci for Identification of Upland Cotton Varieties

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