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Genome‐wide association studies and QTL mapping uncover the genetic architecture of ear tip‐barrenness in maize
Author(s) -
Li Zhaoling,
Liu Peng,
Zhang Xiaoxiang,
Zhang Yinchao,
Ma Langlang,
Liu Min,
Guan Zhongrong,
Zhang Yanling,
Li Peng,
Zou Chaoying,
He Yongcong,
Gao Shibin,
Pan Guangtang,
Shen Yaou
Publication year - 2020
Publication title -
physiologia plantarum
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.351
H-Index - 146
eISSN - 1399-3054
pISSN - 0031-9317
DOI - 10.1111/ppl.13087
Subject(s) - quantitative trait locus , biology , genetic architecture , genome wide association study , linkage disequilibrium , single nucleotide polymorphism , genetics , association mapping , family based qtl mapping , genetic association , candidate gene , snp , allele , haplotype , chromosome , gene mapping , gene , genotype
Ear tip‐barrenness (ETB) phenotype threatens crop yield, because it reduces the kernel number per ear. The genetic basis of ETB in maize remains largely unknown. Herein, a genome‐wide association study (GWAS) and quantitative trait loci (QTL) mapping were jointly applied to identify the significant genetic loci interrelated with ETB. Six significant SNPs were detected at a stringent P ‐value threshold (1.95 × 10 −6 ). Additionally, four environment‐stable SNPs were co‐detected across a single environment and best linear unbiased prediction (BLUP) model at a less stringent P ‐value threshold (1 × 10 −4 ). The above 10 SNPs were closely linked to 6 candidate genes, which mainly involved seed development, photosynthesis and ethylene response. Moreover, the ratio of superior allele at each significant SNP ranged from 0 to 83.33% in 30 investigated maize elite lines. QTL mapping identified 14 QTL with phenotypic variation explained (PVE) ranging from 3.64 to 7.09%, of which one QTL (qETB2‐1) was repeatedly identified in two environments. Combined analysis of GWAS and QTL mapping showed that one SNP (PZE‐102175229, chromosome 2: 217 66 Mb) was located in the QTL (qETB2‐2, chromosome 2: 215 90–217 82 Mb). Eighteen gene models situated in the linkage disequilibrium (LD) region of the co‐localized SNP were further used to evaluate their correlation with ETB by candidate gene association analysis. Two superior haplotypes and two superior alleles were detected among 74 lines for Zm00001d007195, Zm00001d007197 and Zm00001d007201. These results provide more information for clarifying the molecular mechanism of ETB and for speeding up the genetic improvement of maize varieties.