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作物学报 ›› 2019, Vol. 45 ›› Issue (6): 872-878.doi: 10.3724/SP.J.1006.2019.83067

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于高通量测序开发玉米高效KASP分子标记

陆海燕1,周玲1,林峰1,王蕊2,王凤格2,赵涵1,*()   

  1. 1 江苏省农业科学院 / 江苏省农业生物学重点实验室, 江苏南京 210014
    2 北京市农林科学院玉米研究中心, 北京 100097
  • 收稿日期:2018-10-07 接受日期:2019-01-19 出版日期:2019-06-12 网络出版日期:2019-06-12
  • 通讯作者: 赵涵
  • 作者简介:E-mail: luhaiyan@jaas.ac.cn, Tel: 025-84391957
  • 基金资助:
    本研究由国家重点研发计划项目(2017YFD0101205, 2017YFD0102005);江苏省农业科技自主创新项目(CX(18)1001)

Development of efficient KASP molecular markers based on high throughput sequencing in maize

Hai-Yan LU1,Ling ZHOU1,Feng LIN1,Rui WANG2,Feng-Ge WANG2,Han ZHAO1,*()   

  1. 1 Provincial Key Laboratory of Agrobiology / Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2 Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
  • Received:2018-10-07 Accepted:2019-01-19 Published:2019-06-12 Published online:2019-06-12
  • Contact: Han ZHAO
  • Supported by:
    This study was supported by the National Key Research and Development Program(2017YFD0101205, 2017YFD0102005);the Jiangsu Agricultural Science and Technology Innovation Fund [CX(18)1001].(CX(18)1001)

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摘要：

SNP (Single Nucleotide Polymorphism)在基因组中数量多、分布广, 适用于大规模、自动化基因型检测。本研究利用205份不同来源的玉米自交系全基因组重测序数据鉴定出一系列多态性高的二态性SNP位点并开发出700个KASP分子标记。其中, 202个在46个玉米代表系中得到验证的KASP标记进一步用于系统进化树构建及群体结构分析。结果显示, 开发成功的KASP标记在染色体上分布均匀, 平均PIC为0.463, 平均MAF为0.451。基于KASP标记位点和总SNP位点的聚类分析结果高度吻合。KASP标记位点与总SNP位点的遗传距离相似性系数高达89.5%, 能成功区分玉米的杂种优势群。该KASP标记可在玉米种质资源分析、连锁群构建以及杂种优势群划分等方面发挥重要作用。

关键词: 玉米, 重测序, KASP标记, 种质资源

Abstract:

SNP (Single Nucleotide Polymorphism) which is abundant and dispersed widely in the genome is suitable for large-scale and automated genotyping. In this study, highly polymorphic bi-allelic SNP loci were screened and 700 KASP (Kompetitive Allele Specific PCR) molecular markers were developed based on resequencing data of 205 diverse maize inbred lines. Among them, 202 KASP markers validated by 46 representative lines were further used for phylogenetic tree construction and genetic structure analysis. The validated KASP markers distributed evenly on 10 chromosomes in maize with an average PIC of 0.463 and an average MAF of 0.451. The phylogenetic tree constructed by KASP markers is highly consistent with that by re-sequencing data. In addition, the genetic similarity coefficient evaluated between KASP loci and the total SNP loci achieved 89.5% which demonstrated the availability of KASP in heterotic group division. These findings suggest that 202 KASP markers play an important role in analysis of germplasm resource, construction of genetic map, and division of heterotic group in maize.

Key words: maize, resequencing, KASP markers, germplasm

表1

实验材料详细信息"

类群
Group		 205份供试材料
205Experimental cultivars		 用于KASP验证的46份材料
46 cultivars for KASP
样本
大小
Size		 占总样本比例
Percentage
(%)		 样本
大小
Size		 占总样本比例 Percentage
(%)		 代表自交系
Representative inbred lines
瑞德
Reid		 14 6.86 4 8.69 B73, A632, 郑32, H84
B73, A632, Zheng 32, H84
改良瑞德Improved Reid 33 16.09 9 19.57 郑58, 478, 5003, 黄C, 1205A, 综3, 铁7922, K22
Zheng 58, 478, 5003, Huang C, 1205A, Zong 3, Tie 7922, K22
热带
Tropic		 18 8.78 8 17.39 苏湾1611, 四路糯, CML162, DY206, CML52, Ki11, Ki3
Suwan 1611, Silunuo, CML162, DY206, CML52, Ki11, Ki3
PB 22 10.73 7 15.22 T877, 齐319, P138, 沈137, 沈135, Yu 87-1
T877, Qi 319, P138, Shen 137, Shen 135, Yu 87-1
兰卡斯特
Lancaster		 50 24.39 6 13.04 Mo17, OH43, LH51, LH61, LH54, 龙抗11
Mo17, OH43, LH51, LH61, LH54, Longkang 11
四平头
Sipingtou		 45 21.95 9 19.57 黄早四, 昌7-2, S22, Huangyesi 3, Wu 126, 444, K12
Huangzaosi, Chang 7-2, S22, Huangyesi 3, Wu 126, 444, K12
其他Other 23 11.22 3 6.52 F2, F7

图1

KASP标记基因分型图 a~d为编号不同的KASP标记的基因分型图; AA: 红色簇状是具有HEX型等位基因的品种; GG: 蓝色簇状是具有FAM型等位基因的品种; NTC: 是不含模板的空白对照。"

图2

202个SNP位点遗传多态性 A: 202个SNP位点在染色体上的物理位置, 右边数字是202个KASP标记的编号, 左边数字是202个KASP标记在染色体上物理位置, 单位为Mb; B: 202个SNP位点的最小等位基因频率分布(MAF)和多态信息含量分布(PIC)。"

图3

Neighbor-joining (N-J)树分析 A: 205份自交系基于202个位点的Neighbor-Joining (N-J)树分析, 红色线条代表46个实验材料; B: 205份自交系基于1,660,336个位点的Neighbor-Joining (N-J)树分析; Group 1~Group 7分别代表瑞德群、改良瑞德群、热带群、PB群、兰卡斯特群、四平头群、其他纬度种质。"

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