A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

doi:10.1016/S2095-3119(14)60902-3

Journal of Integrative Agriculture ›› 2015, Vol. 14 ›› Issue (9): 1697-1705.DOI: 10.1016/S2095-3119(14)60902-3

A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

ZHAI Hui-jie, FENG Zhi-yu, LIU Xin-ye, CHENG Xue-jiao, PENG Hui-ru, YAO Ying-yin, SUN Qi-xin, NI Zhong-fu

State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Key Laboratory of Crop Genomics and Genetic Improvement, Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement, National Plant Gene Research Centre (Beijing), China Agricultural University, Beijing 100193, P.R.China

收稿日期:2014-09-03 出版日期:2015-09-03 发布日期:2015-09-05
通讯作者: NI Zhong-fu, Tel: +86-10-62734421,E-mail: nizf@cau.edu.cn
作者简介:ZHAI Hui-jie, Tel: +86-10-62734421, E-mail: huijiezhai@gmail.com;
基金资助:
This work was financially supported by the National Natural Science Foundation of China (91435204, 31271710), the National 863 Program of China (2012AA10A309), and the Program of Conservation and Sustainable Utilization of Wild Relatives of Crops by the Ministry of Agriculture of China (201003021).

A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

ZHAI Hui-jie, FENG Zhi-yu, LIU Xin-ye, CHENG Xue-jiao, PENG Hui-ru, YAO Ying-yin, SUN Qi-xin, NI Zhong-fu

State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Key Laboratory of Crop Genomics and Genetic Improvement, Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement, National Plant Gene Research Centre (Beijing), China Agricultural University, Beijing 100193, P.R.China

Received:2014-09-03 Online:2015-09-03 Published:2015-09-05
Contact: NI Zhong-fu, Tel: +86-10-62734421,E-mail: nizf@cau.edu.cn
About author:ZHAI Hui-jie, Tel: +86-10-62734421, E-mail: huijiezhai@gmail.com;
Supported by:
This work was financially supported by the National Natural Science Foundation of China (91435204, 31271710), the National 863 Program of China (2012AA10A309), and the Program of Conservation and Sustainable Utilization of Wild Relatives of Crops by the Ministry of Agriculture of China (201003021).

摘要/Abstract

摘要： The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1, 703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

关键词: wheat , genetic linkage map , SNP , SSR , unigene , deletion bin-mapped ESTs

Abstract: The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1, 703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

Key words: wheat , genetic linkage map , SNP , SSR , unigene , deletion bin-mapped ESTs

ZHAI Hui-jie, FENG Zhi-yu, LIU Xin-ye, CHENG Xue-jiao, PENG Hui-ru, YAO Ying-yin, SUN Qi-xin, NI Zhong-fu. A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)[J]. Journal of Integrative Agriculture, 2015, 14(9): 1697-1705.

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A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

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