Characterization and fine mapping of qkrnw4, a major QTL controlling kernel row number in maize

• Published in: Theoretical and applied genetics Vol. 132; no. 12; pp. 3321 - 3331
• Main Authors: Nie, Ningning, Ding, Xiaoyu, Chen, Lin, Wu, Xun, An, Yixin, Li, Chunhui, Song, Yanchun, Zhang, Dengfeng, Liu, Zhizhai, Wang, Tianyu, Li, Yu, Li, Yong-xiang, Shi, Yunsu
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.12.2019; Springer; Springer Nature B.V
• Subjects: Agriculture; Analysis; Association analysis; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Biotechnology; Chromosome Mapping; Corn; Crop yields; Gene mapping; Genes; Genetic aspects; Genetic diversity; Genetic Linkage; Inbreeding; Life Sciences; Linkage analysis; Original Article; Phenotype; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Quantitative genetics; Quantitative Trait Loci; Seeds - genetics; Zea mays - genetics; Netherlands; China
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-019-03427-9

Key message A major QTL controlling kernel row number, qkrnw4 , was identified by combining linkage analysis and association mapping. Within qkrnw4 , on the basis of its expression and bioinformatics analysis, Zm00001d052910 was supposed to be the candidate gene for kernel row number. Kernel row number (KRN) is an important yield-related trait that affects kernel number in maize. Understanding the genetic basis of KRN is important for increasing maize yields. In the present study, by the use of a near-isogenic line (NIL) that has a B73 background and that consistently displays a low KRN across environments, qkrnw4 , a major quantitative trait locus (QTL) associated with KRN within a yield trait-related QTL hotspot in bin 4.08, was finely mapped to an ~ 33-kb interval. Regional association analysis of a nested association mapping population comprising 5000 recombinant inbred lines revealed Zm00001d052910, which encodes a protein with an unknown function, as the important candidate gene responsible for qkrnw4 . Different expression levels of this candidate gene in immature ears were detected between the NIL and its recurrent parent. Moreover, the expression of several auxin-related genes was consistent with that of the candidate gene. Furthermore, the potential associations of this candidate gene with well-known inflorescence-related genes were discussed. The results of this study provide important information for the genetic elucidation of KRN variation in maize.