
基于全基因组SNP构建甘蓝型油菜指纹图谱
Construction of fingerprint for Brassica napus germplasm by genome-wide SNPs
甘蓝型油菜是世界上重要的油料作物,可用作油料、饲料以及食品等,具有较高的经济价值。为了高效快速地鉴定并区分油菜品种,加强油菜品种管理,本试验利用505份油菜种质的重测序数据进行SNP鉴定,根据杂合率、位点缺失率以及多态性等指标对SNP集合进行筛选,得到了能够高效鉴定油菜种质的核心SNP位点组合,构建了DNA指纹图谱。该套核心位点组合包括897个位点,其MAF、PIC的平均值分别为0.41、0.474。使用该套SNP位点组合进行品种区分,每两个材料之间的差异位点数目90%为357~508。对核心SNP位点进行精简,最少用17个SNP 标记可完全鉴定该套种质。本研究使用高质量的油菜重测序数据,筛选出了897个核心SNP位点,并利用该套核心SNP组合构建了油菜的特征指纹图谱,为油菜遗传多样性分析、品种鉴定以及种质管理提供数据参考。
As an important oil crop, Brassica napus provides raw material for vegetable oil and extraction meal as feed, food and fuel worldwide, and has a high economic value. To efficiently identify rapeseed varieties and improve the management of rapeseed varieties, we performed genome-wide re-sequencing for 505 B. napus accessions and identified a core set of SNPs for DNA fingerprint construction. A total of 897 core SNPs were obtained after strict filtering. Detection of 505 B. napus accessions using these 897 core SNPs combination, the average value of MAF was 0.41, and the average polymorphism information content was 0.474. There was at least one different locus between B. napus accessions pairs, and 90% pairs showed 357-508 different loci. Based on these core SNPs, the fingerprint was constructed. Moreover, we obtained the simplified 17 SNPs by reducing the SNP markers, which could fully identify the set of 505 B. napus germplasm. This study provides a reference for genetic diversity analysis, molecular identification and genetic improvement in B. napus.
甘蓝型油菜 / 群体基因组重测序 / SNP / DNA指纹图谱 {{custom_keyword}} /
Brassica napus / whole-genome resequencing / SNP / DNA fingerprint {{custom_keyword}} /
表1 各筛选步骤中的SNP数量Table 1 The number of SNPs in each filtering step |
过滤步骤 Filtering step | SNP数量 The number of SNP markers |
---|---|
raw data | 9 970 990 |
remove scaffold SNPs | 8 220 713 |
MAF>0.2 | 1 838 956 |
het<0.05 | 1 373 962 |
geno<0.05 | 496 699 |
Imputation | 496 699 |
remove intergenic SNPs | 373 406 |
MAF>0.3 | 219 772 |
het<0.01 | 18 244 |
LD<0.2 | 897 |
图1 897个核心SNP在染色体上的位置Fig. 1 Position of 897 core SNPs on chromosomes |
表2 统计各染色体上的核心SNP位点Table 2 Statistics of the core SNPs on chromosomes |
染色体 Chromosome | 标记数 Number of markers | 染色体长度 Length /Mb | 分布密度 Density /(kb/SNP) | 染色体 Chromosome | 标记数 Number of markers | 染色体长度 Length /Mb | 分布密度 Density/(kb/SNP) |
---|---|---|---|---|---|---|---|
A01 | 24 | 38.0 | 1 583.5 | C01 | 31 | 57.9 | 1 867.1 |
A02 | 33 | 35.9 | 1 089.2 | C02 | 25 | 65.3 | 2 611.8 |
A03 | 75 | 44.9 | 598.2 | C03 | 64 | 79.1 | 1 235.3 |
A04 | 51 | 25.7 | 503.5 | C04 | 74 | 71.2 | 961.9 |
A05 | 45 | 46.0 | 1 022.0 | C05 | 48 | 59.6 | 1 240.6 |
A06 | 63 | 48.7 | 773.1 | C06 | 39 | 52.5 | 1 346.5 |
A07 | 46 | 32.3 | 702.2 | C07 | 59 | 61.0 | 1 033.7 |
A08 | 31 | 28.3 | 913.8 | C08 | 51 | 53.7 | 1 052.2 |
A09 | 54 | 65.9 | 1 219.7 | C09 | 28 | 68.4 | 2 443.5 |
A10 | 56 | 26.6 | 474.9 | total | 419 | 568.5 | 1 356.9 |
total | 478 | 392.3 | 820.7 |
图3 油菜两两材料间差异位点数分布情况Fig. 3 Distribution of the number of different sites between B. napus accession pairs |
图4 品种识别率变化曲线图Fig. 4 Recognition rate of SNP combinations with different number of SNPs |
图5 505份油菜DNA指纹图谱Fig. 5 DNA fingerprints from 505 B. napus germplasm |
表3 精简后的17个核心SNP标记信息Table 3 Information of the 17 simplified core SNPs in detecting 505 B. napus germplasm |
SNP编号 SNP ID | 染色体 Chromosome | 位置 Position /bp | 等位基因 A Allele A | 等位基因 B Allele B |
---|---|---|---|---|
1 | A03 | 4 294 160 | G | C |
2 | A03 | 23 310 934 | T | C |
3 | A05 | 872 945 | A | T |
4 | A07 | 18 469 370 | T | C |
5 | A09 | 57 259 238 | C | T |
6 | A10 | 18 527 388 | A | T |
7 | A10 | 21 039 076 | G | A |
8 | C02 | 23 742 881 | T | C |
9 | C03 | 65 838 150 | C | T |
10 | C03 | 70 516 306 | C | T |
11 | C04 | 1 911 594 | C | T |
12 | C04 | 28 626 338 | T | C |
13 | C05 | 11 671 173 | C | T |
14 | C06 | 21 453 185 | A | G |
15 | C07 | 46 771 071 | A | G |
16 | C08 | 36 762 293 | A | C |
17 | C08 | 45 178 626 | C | T |
1 |
黎咏蜀. 饲用油菜栽培技术及营养价值研究[D]. 重庆: 西南大学, 2014.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
2 |
中国统计年鉴[M]. 北京:中国统计出版社, 2020.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
3 |
刘成, 冯中朝, 肖唐华, 等. 我国油菜产业发展现状、潜力及对策[J]. 中国油料作物学报, 2019, 41(4): 485-489. DOI:10.7505/j.issn.1007-9084.2019.04.001 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
4 |
李利霞, 陈碧云, 闫贵欣, 等. 中国油菜种质资源研究利用策略与进展[J]. 植物遗传资源学报, 2020, 21(1): 1-19. DOI:10.13430/j.cnki.jpgr.20200109005 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
5 |
杨勇. 甘蓝型油菜遗传多样性分析及核心亲本的指纹图谱构建[D]. 武汉: 华中农业大学, 2013.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
6 |
刘可心. 利用SNP芯片构建玉米DNA指纹技术的初步研究[D]. 长春: 吉林农业大学, 2016.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
7 |
田红丽, 杨扬, 王璐, 等. 兼容型maizeSNP384标记筛选与玉米杂交种DNA指纹图谱构建[J]. 作物学报, 2020, 46(7): 1006-1015. DOI:10.3724/SP.J.1006.2020.93048 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
8 |
李乐晨, 朱国忠, 苏秀娟, 等. 适于海岛棉指纹图谱构建的SNP核心位点筛选与评价[J]. 作物学报, 2019, 45(5): 647-655. DOI:10.3724/SP.J.1006.2019.84123 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
9 |
赵仁欣, 李森业, 郭瑞星, 等. 利用SNP芯片构建我国冬油菜参试品种DNA指纹图谱[J]. 作物学报, 2018, 44(7): 956-965. DOI:10.3724/SP.J.1006.2018.00956 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
10 |
唐立群, 肖层林, 王伟平. SNP分子标记的研究及其应用进展[J]. 中国农学通报, 2012, 28(12): 154-158. DOI:10.3969/j.issn.1000-6850.2012.12.028 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
11 |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
12 |
王凤格,赵久然,杨扬.基于遗传算法的植物品种真实性鉴定位点筛选方法[P]. 中国发明专利, ZL201310629676.2. 2013.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
13 |
李梓榕, 袁雄, 陈叶, 等. 基于全基因组SNP高效鉴定水稻种质资源并构建指纹图谱[J]. 分子植物育种, 2020, 18(18): 6050-6057. DOI:10.13271/j.mpb.018.006050 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
14 |
李志远, 于海龙, 方智远, 等. 甘蓝SNP标记开发及主要品种的DNA指纹图谱构建[J]. 中国农业科学, 2018, 51: 2771-2788.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
15 |
张青松, 廖庆喜, 肖文立, 等. 油菜种植耕整地技术装备研究与发展[J]. 中国油料作物学报, 2018, 40(5): 702-711. DOI:10.7505/j.issn.1007-9084.2018.05.013 .
{{custom_citation.content}}
{{custom_citation.annotation}}
|
16 |
匡猛, 杨伟华, 许红霞, 等. 中国棉花主栽品种DNA指纹图谱构建及SSR标记遗传多样性分析[J]. 中国农业科学, 2011, 44: 20-27.
{{custom_citation.content}}
{{custom_citation.annotation}}
|
17 |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
{{custom_ref.label}} |
{{custom_citation.content}}
{{custom_citation.annotation}}
|
/
〈 |
|
〉 |