Identification of QTL for resistance to leaf blast in foxtail millet by genome re-sequencing analysis
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ORIGINAL ARTICLE
Identification of QTL for resistance to leaf blast in foxtail millet by genome re‑sequencing analysis Bohong Tian1 · Lixin Zhang1 · Yanli Liu1 · Peipei Wu2 · Wei Wang1 · Yue Zhang1 · Hongjie Li2 Received: 20 April 2020 / Accepted: 13 November 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message Three QTL for resistance to leaf blast were identified on chromosomes 1, 2, and 8 of the foxtail millet cultivar Yugu 5. Abstract Leaf blast disease of foxtail millet (Setaria italica) is caused by Pyricularia spp., can infect all the aboveground parts of plants, and is the most frequently observed blast disease in China. Lack of information on genetic control of disease resistance impedes developing leaf blast-resistant cultivars. An F 6 recombinant inbred line (RIL) population from the cross Yugu 5 × Jigu 31 was phenotyped for its reactions to leaf blast in six field trials in the naturally diseased nurseries. An ultra-density genetic linkage map was constructed using 35,065 single nucleotide polymorphism (SNP) markers generated by sequencing of the RIL population. Three QTL, QLB-czas1, QLB-czas2, and QLB-cazas8, were detected in the genomic intervals of 276.6 kb, 1.62 Mb, and 1.75 Mb on chromosomes 1, 2, and 8 of Yugu 5, which explained 14–17% (2 environments), 9% (5 environments), and 12–20% (6 environments) of the phenotypic variations. Bulked segregant analysis (BSA) and RNA sequencing (BSR-Seq) method identified common SNPs that fell in the genomic region of QLB-czas8, providing additional evidence of localization of this QTL. Three and 19 predicted genes were annotated to be associated with disease resistance in the genomic intervals for QLB-czas2 and QLB-czas8. Due to their unique positions, these QTL appear to be new loci conferring resistance to leaf blast. The identification of these new resistance QTL will be useful in cultivar development and the study of the genetic control of blast resistance in foxtail millet.
Introduction Foxtail millet [Setaria italica (L.) Beauv.] has been cultivated as a staple food crop in China for thousands of years (Yang et al. 2012). It is well known for its adaptability to diverse agro-ecological conditions, especially in fields with Communicated by Hai-Chun Jing. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03730-w) contains supplementary material, which is available to authorized users. * Bohong Tian [email protected] * Hongjie Li [email protected] 1
Cangzhou Academy of Agricultural and Forestry Sciences, Cangzhou 061001, China
The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
2
poor nutrition and semi-dry environments (Dwivedi et al. 2012). This small grained cereal crop is also consumed for food and feed in other countries of East Asia, the Americans, Africa, and Europe (Singh et al. 2017a). Among various diseases that occur in foxtail millet
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