Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing

摘要

Background The maize kernel row number (KRN) is a key component that contributes to grain yield and has high broad-sense heritability ( H 2 ). Quantitative trait locus/loci (QTL) mapping using a high-density genetic map is a powerful approach to detecting loci that are responsible for traits of interest. Bulked segregant ribonucleic acid (RNA) sequencing (BSR-seq) is another rapid and cost-effective strategy to identify QTL. Combining QTL mapping using a high-density genetic map and BSR-seq may dissect comprehensively the genetic architecture underlying the maize KRN. Results A panel of 300?F₂ individuals derived from inbred lines abe2 and B73 were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 4,579 high-quality polymorphic SLAF markers were obtained and used to construct a high-density genetic map with a total length of 2,123 centimorgan (cM) and an average distance between adjacent markers of 0.46?cM. Combining the genetic map and KRN of F₂ individuals, four QTL ( qKRN1 , qKRN2 , qKRN5 , and qKRN8-1 ) were identified on chromosomes 1, 2, 5, and 8, respectively. The physical intervals of these four QTL ranged from 4.36?Mb for qKRN8-1 to 7.11?Mb for qKRN1 with an average value of 6.08?Mb. Based on high-throughput sequencing of two RNA pools bulked from leaves of plants with extremely high and low KRNs, two QTL were detected on chromosome 8 in the 10–25?Mb ( BSR_QTL1 ) and 60–150?Mb ( BSR_QTL2 ) intervals. According to the physical positions of these QTL, qKRN8-1 was included by BSR_QTL2 . In addition, qKRN8-1 was validated using QTL mapping with a recombinant inbred lines population that was derived from inbred lines abe2 and B73. Conclusions In this study, we proved that combining QTL mapping using a high-density genetic map and BSR-seq is a powerful and cost-effective approach to comprehensively revealing genetic architecture underlying traits of interest. The QTL for the KRN detected in this study, especially qKRN8-1 , can be used for performing fine mapping experiments and marker-assisted selection in maize breeding.