[1]朱小品,徐婷婷,孟珊,等.基于核心KASP标记的江苏粳稻品种DNA指纹图谱构建[J].江苏农业学报,2024,(09):1569-1585.[doi:doi:10.3969/j.issn.1000-4440.2024.09.001]
　ZHU Xiaopin,XU Tingting,MENG Shan,et al.Construction of DNA fingerprint for japonica rice varieties in Jiangsu based on core KASP markers[J].,2024,(09):1569-1585.[doi:doi:10.3969/j.issn.1000-4440.2024.09.001]
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基于核心KASP标记的江苏粳稻品种DNA指纹图谱构建()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2024年09期
页码:
1569-1585
栏目:
遗传育种·生理生化
出版日期:
2024-09-30

文章信息/Info

Title:
Construction of DNA fingerprint for japonica rice varieties in Jiangsu based on core KASP markers
作者:
朱小品; 徐婷婷; 孟珊; 杨雪; 杨欣; 朱银; 狄佳春; 郭春滨; 王宁; 颜伟
(江苏省农业科学院种质资源与生物技术研究所/江苏省农业种质资源保护与利用平台/江苏省农业生物学重点实验室,江苏南京210014)
Author(s):
ZHU Xiaopin; XU Tingting; MENG Shan; YANG Xue; YANG Xin; ZHU Yin; DI Jiachun; GUO Chunbin; WANG Ning; YAN Wei
(Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences/Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm/Jiangsu Key Laboratory for Agrobiology, Nanjing 210014, China)
关键词:
水稻; KASP标记; DNA指纹图谱; 品种鉴定; 遗传多样性分析
Keywords:
Oryza sativa L.; KASP marker; DNA fingerprint; cultivar identification; genetic diversity analysis
分类号:
S511.2+2
DOI:
doi:10.3969/j.issn.1000-4440.2024.09.001
文献标志码:
A
摘要:
为了建立江苏粳稻品种DNA指纹图谱数据库,本研究利用水稻10K液相芯片对314份来源广泛的水稻种质资源进行SNP基因分型,筛选出一系列高多态性的SNP位点并开发出122个KASP标记。利用122个KASP标记对38份江苏粳稻品种进行检测,以多态性信息量(PIC)＞0.3,最小等位基因频率(MAF)＞0.2,检出率＞0.9为筛选标准,筛选出56个具有高效鉴别效率的核心KASP标记。遗传距离相关性分析结果表明,基于56个核心KASP标记的江苏粳稻品种的遗传距离与基于122个高多态性KASP标记的的江苏粳稻品种的遗传距离相关系数为89.1%,呈极显著正相关(P＜0.01),表明56个核心标记可以有效代替122个高多态性标记进行品种鉴定。进一步利用56个核心KASP标记对102份江苏粳稻品种的遗传多样性进行分析,并构建了102份品种的DNA指纹图谱和分子身份证二维码,本研究结果为江苏地区粳稻品种鉴定、选育和种质资源高效利用提供了参考。
Abstract:
In order to establish the DNA fingerprinting database of japonica rice varieties in Jiangsu province, SNP genotyping was carried out in 314 rice germplasm resources by using GenoBaits rice 10K panel, a series of SNP loci with high polymorphism were screened and 122 KASP markers were developed. Thirty-eight japonica rice varieties in Jiangsu province were tested with 122 KASP markers, and 56 core KASP markers with high identification efficiency were selected with polymorphism information content (PIC)＞0.3, minor allele frequency (MAF)＞0.2, and detection rate ＞0.9 as screening criteria. The results of genetic distance correlation analysis showed that the correlation coefficient between the genetic distance of Jiangsu japonica rice varieties based on 56 core KASP markers and the genetic distance of Jiangsu japonica rice varieties based on 122 highly polymorphic KASP markers was 89.1%, showing a very significant positive correlation (P＜0.01). The results indicated that 56 core markers could effectively replace 122 highly polymorphic markers for variety identification. The genetic diversity of 102 japonica rice varieties in Jiangsu province was further analyzed by using 56 core KASP markers, and the DNA fingerprints and molecular ID codes of 102 varieties were constructed. The results of this study provide a reference for the identification, breeding and efficient utilization of japonica rice germplasm resources in Jiangsu province.

参考文献/References:

[1]李阳阳,李剑,周欣兴,等. 新时期水稻新品种保护和DUS测试现状与问题探讨[J]. 中国稻米,2024,30(2):51-56.
[2]孔维国,王俊峰,丁汉凤. DNA指纹数据库在我国主要农作物种质资源中的应用[J]. 山东农业科学,2014,46(4):131-135.
[3]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.
[4]王富强,樊秀彩,张颖,等. SNP分子标记在作物品种鉴定中的应用和展望[J]. 植物遗传资源学报,2020,21(5):1308-1320.
[5]ALEXANDROV N, TAI S S, WANG W S, et al. SNP-Seek Database of SNPs derived from 3000 rice genomes [J]. Nucleic Acids Research,2015,43:1023-1027.
[6]CHEN H D, XIE W B, HE H, et al. A high-density SNP genotyping array for rice biology and molecular breeding [J]. Molecular Plant,2014,7(3):541-553.
[7]李巧英. 农作物种子检测中SSR与SNP分子标记方法的比较分析[J]. 中国种业,2021(12):48-50.
[8]中国水稻研究所,中国科学院分子植物科学卓越创新中心,全国农业技术推广服务中心. 水稻品种真实性鉴定SNP标记法:NY/T 2745-2021[S]. 北京:中国农业出版社,2021.
[9]颜廷进,蒲艳艳,张文兰,等. 基于SNP标记的菜豆品种真实性和纯度鉴定技术[J]. 山东农业科学,2019,51(12):111-119.
[10]KUMAR D, CHHOKAR V, SHEORAN S, et al. Characterization of genetic diversity and population structure in wheat using array based SNP markers [J]. Molecular Biology Reports,2020,47(1):293-306.
[11]TAM N T, DWIYANTI M S, KOIDE Y, et al. Profiling SNP and nucleotide diversity to characterize mekong delta rice landraces in southeast asian populations [J]. Plant Genome,2019,12(3):1-11.
[12]TIAN H L, YANG Y, YI H M, et al. New resources for genetic studies in maize (Zea mays L.):a genome-wide Maize6H-60K single nucleotide polymorphism array and its application[J]. Plant Journal,2021,105(4):1113-1122.
[13]孙正文,匡猛,马峙英,等. 利用CottonSNP63K芯片构建棉花品种的指纹图谱[J]. 中国农业科学,2017,50(24):4692-4704.
[14]杨青青,唐家琪,张昌泉,等. KASP标记技术在主要农作物中的应用及展望[J]. 生物技术通报,2022,38(4):58-71.
[15]陆海燕,周玲,林峰,等. 基于高通量测序开发玉米高效KASP分子标记[J]. 作物学报,2019,45(6):872-878.
[16]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.
[17]石晗,陈子义,陈珏,等. 54份蚕豆种质资源主要农艺性状的综合鉴定与评价[J]. 江苏农业科学,2023,51(20):67-76.
[18]周玉杰,贺治洲,林秋云,等. 热带水稻种质资源全生育期耐盐性鉴定与评价[J]. 南方农业学报,2023,54(7):1944-1952.
[19]许园园,邢苗苗,严继勇,等. 甘蓝黑腐病致病菌分离与种质资源抗性鉴定[J]. 江苏农业科学,2022,50(10):98-103.
[20]周彩霞,罗培四,孔方南,等. 木奶果种质资源的遗传多样性分析及DNA指纹图谱构建 [J]. 南方农业学报,2022,53(5):1207-1215.
[21]马小定,崔迪,韩冰,等. 水稻种质资源全基因组DNA指纹鉴定方法研究[J]. 植物遗传资源学,2023,24(4):1106-1113.
[22]CASTELLANA S, RANZINO L, BERITOGNOLO I, et al. Genetic characterization and molecular fingerprint of traditional umbrian tomato (Solanum lycopersicum L.) landraces through SSR markers and application for varietal identification[J]. Genetic Resources and Crop Evolution,2020,67(7):1807-1820.
[23]HUANG X H, HAN B. Natural variations and genome-wide association studies in crop plants [J]. Annual Review of Plant Biology,2014,65:531-551.
[24]SEMAGN K, BABU R, HEARNE S, et al. Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP):overview of the technology and its application in crop improvement [J]. Molecular Breeding,2014，33(1):1-14.
[25]魏中艳,李慧慧,李骏,等. 应用SNP精准鉴定大豆种质及构建可扫描身份证[J]. 作物学报,2018,44(3):315-323.
[26]孔维国,王俊峰,丁汉凤,等. DNA指纹数据库在我国主要农作物种质资源中的应用[J]. 山东农业科学,2014,46(4):131-135.
[27]吴则东,江伟,马龙彪. 分子标记技术在农作物品种鉴定上的研究进展及未来展望[J]. 中国农学通报,2015,31(33):172-176.

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备注/Memo

备注/Memo:
收稿日期：2024-04-27基金项目：江苏省自然科学青年基金项目(BK20210151)；江苏省种质资源精准鉴定评价项目(005012691230229)作者简介：朱小品(1989-),女,河南商丘人,博士,助理研究员,主要从事水稻种质资源遗传多样性及种子休眠与萌发的生物学机理研究。(E-mail)zxp1028@126.com通讯作者：颜伟,(E-mail)yanwei@jaas.ac.cn
更新日期/Last Update: 2024-11-17