中国农业科学 ›› 2020, Vol. 53 ›› Issue (16): 3333-3343.doi: 10.3864/j.issn.0578-1752.2020.16.011
收稿日期:
2019-12-30
接受日期:
2020-06-10
出版日期:
2020-08-16
发布日期:
2020-08-27
通讯作者:
王昆,丛佩华
作者简介:
高源,E-mail:基金资助:
GAO Yuan(),WANG DaJiang,WANG Kun(
),CONG PeiHua(
),LI LianWen,PIAO JiCheng
Received:
2019-12-30
Accepted:
2020-06-10
Online:
2020-08-16
Published:
2020-08-27
Contact:
Kun WANG,PeiHua CONG
摘要:
【目的】基于高通量简化基因组测序技术在全基因组开发的SNP标记,对中国原产苹果属植物种内和种间的亲缘关系和群体遗传结构解析,为苹果属植物的起源演化以及系统分类提供理论依据。【方法】对427份15种中国原产苹果属植物种质资源进行高通量简化基因组测序(SLAF-seq),基于获得的SLAF标签,利用BWA软件将其通过比对定位到参考基因组上并获得多态性SLAF标签;利用GATK和SAMtools两种方法在多态性SLAF中开发多态性单核苷酸(SNP),筛选两种方法共同得到的SNP作为开发的SNP标记数据集。根据完整度>0.94、次要等位基因频率(MAF)>0.05过滤筛选获得多态性的SNP。基于筛选多态性SNP,使用MEGA7的NJ(neighbor-joining)算法,构建苹果属不同种的系统进化树。利用Admixture软件进行群体遗传结构分析,假设样品的分群数(K)为1—15进行聚类,根据交叉验证错误率确定最佳K值,解析苹果属不同种间和种内的遗传结构。【结果】通过SLAF-seq技术对427份苹果属植物种质进行测序,最终获得586 454个SLAF标签,其中多态性SLAF标签463 612个。经过序列比对分析和筛选得到46 460个SNP位点,基于这些SNP位点构建苹果属植物不同种的系统发生树并分析群体结构。系统发育分析将15种苹果属植物分成4个类群,群体遗传结构在K=5和K=14为两个分群关键点。综合两种分析方法的结果,15种苹果属植物可分为4个基本的类群,分别为山荆子类群,新疆野苹果和少数中国苹果类群,变叶海棠、花叶海棠、陇东海棠、山楂海棠、滇池海棠和沧江海棠类群,4个苹果属植物栽培种中国苹果、八棱海棠、花红和楸子类群。中国苹果的部分种质中有新疆野苹果和山荆子的基因背景,但其中还有一部分种质可以独立代表类群基因库,其基因库中并没有新疆野苹果的参与,而与山荆子、花红、楸子和八棱海棠密切相关。【结论】利用SLAF技术快速发掘覆盖全基因组的46 460个多态性SNP标记可有效地对中国原产苹果属植物种内和种间的亲缘关系及遗传结构进行研究,为苹果属植物种质资源的鉴定评价、遗传多样性、系统分类和起源演化提供参考。15种苹果属植物分为4个基本类群,苹果属植物野生种和栽培种分类群明显,中国苹果与其他栽培种的亲缘关系密切。
高源,王大江,王昆,丛佩华,李连文,朴继成. 基于高密度SNP标记的苹果属15种植物资源的亲缘关系与遗传结构分析[J]. 中国农业科学, 2020, 53(16): 3333-3343.
GAO Yuan,WANG DaJiang,WANG Kun,CONG PeiHua,LI LianWen,PIAO JiCheng. Genetic Relationship and Structure Analysis of 15 Species of Malus Mill. Based on SNP Markers[J]. Scientia Agricultura Sinica, 2020, 53(16): 3333-3343.
表1
用于SLAF测序分析的15个种苹果属植物种质资源"
序号 Code | 供试种 Species | 来源地 Origin | 数量 Number | 序号 Code | 供试种 Species | 来源地 Origin | 数量 Number | |
---|---|---|---|---|---|---|---|---|
1 | 新疆野苹果 Malus sieversii | 新疆 Xinjiang | 161 | 5 | 花红 Malus asiatica | 黑龙江 Heilongjiang | 7 | |
2 | 中国苹果 Malus domestica subsp.chinensis | 新疆 Xinjiang | 2 | 甘肃 Gansu | 1 | |||
黑龙江 Heilongjiang | 2 | 河北 Hebei | 9 | |||||
甘肃 Gansu | 4 | 云南 Yunnan | 1 | |||||
河北 Hebei | 14 | 6 | 八棱海棠 Malus robusta | 河北 Hebei | 32 | |||
山西 Shanxi | 10 | 山西 Shanxi | 1 | |||||
山东 Shandong | 1 | 吉林 Jilin | 1 | |||||
3 | 山荆子 Malus baccata | 黑龙江 Heilongjiang | 47 | 7 | 陇东海棠 Malus kansuensis | 甘肃 Gansu | 4 | |
甘肃 Gansu | 3 | 8 | 垂丝海棠 Malus halliana | 甘肃 Gansu | 9 | |||
河北 Hebei | 10 | 9 | 山楂海棠 Malus komarovii | 吉林 Jilin | 1 | |||
山西 Shanxi | 14 | 10 | 变叶海棠 Malus toringoides | 四川 Sichuan | 2 | |||
内蒙古 Inner Mongolia | 41 | 云南 Yunnan | 1 | |||||
吉林 Jilin | 19 | 11 | 花叶海棠 Malus transitoria | 四川 Sichuan | 1 | |||
4 | 楸子 Malus prunifolia | 黑龙江 Heilongjiang | 5 | 12 | 丽江山荆子 Malus rockii | 云南 Yunnan | 1 | |
甘肃 Gansu | 4 | 13 | 滇池海棠 Malus yunnanensis | 云南 Yunnan | 1 | |||
河北 Hebei | 2 | 14 | 湖北海棠 Malus hupehensis | 云南 Yunnan | 1 | |||
山西 Shanxi | 8 | 15 | 沧江海棠 Malus ombrophila | 云南 Yunnan | 1 | |||
内蒙古 Inner Mongolia | 1 | |||||||
吉林 Jilin | 5 |
表2
基于SNP的苹果属植物15个种间的遗传距离"
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 0.000 | ||||||||||||||
2 | 0.030 | 0.000 | |||||||||||||
3 | 0.970 | 1.000 | 0.000 | ||||||||||||
4 | 0.600 | 0.606 | 0.394 | 0.000 | |||||||||||
5 | 0.030 | 0.000 | 1.000 | 0.606 | 0.000 | ||||||||||
6 | 0.030 | 0.000 | 1.000 | 0.606 | 0.000 | 0.000 | |||||||||
7 | 0.030 | 0.000 | 1.000 | 0.606 | 0.000 | 0.000 | 0.000 | ||||||||
8 | 0.187 | 0.167 | 0.833 | 0.571 | 0.167 | 0.167 | 0.167 | 0.000 | |||||||
9 | 0.030 | 0.000 | 1.000 | 0.606 | 0.000 | 0.000 | 0.000 | 0.167 | 0.000 | ||||||
10 | 0.953 | 0.981 | 0.019 | 0.398 | 0.981 | 0.981 | 0.981 | 0.821 | 0.981 | 0.000 | |||||
11 | 0.143 | 0.120 | 0.880 | 0.581 | 0.120 | 0.120 | 0.120 | 0.247 | 0.120 | 0.866 | 0.000 | ||||
12 | 0.030 | 0.000 | 1.000 | 0.606 | 0.000 | 0.000 | 0.000 | 0.167 | 0.000 | 0.981 | 0.120 | 0.000 | |||
13 | 0.134 | 0.111 | 0.889 | 0.582 | 0.111 | 0.111 | 0.111 | 0.241 | 0.111 | 0.874 | 0.204 | 0.111 | 0.000 | ||
14 | 0.279 | 0.265 | 0.735 | 0.550 | 0.265 | 0.265 | 0.265 | 0.343 | 0.265 | 0.727 | 0.321 | 0.265 | 0.317 | 0.000 | |
15 | 0.030 | 0.000 | 1.000 | 0.606 | 0.000 | 0.000 | 0.000 | 0.167 | 0.000 | 0.981 | 0.120 | 0.000 | 0.111 | 0.265 | 0.000 |
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