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

Abstract

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.

Keywords: Bulked segregant RNA sequencing; Kernel row number; Maize; Specific-locus amplified fragment sequencing.

Fig. 1

Distribution of polymorphic SLAF markers used to construct genetic map and correlation between genetic position and physical position of markers

Fig. 2

The QTL for the KRN identified in the F₂ population using a high-density genetic map

Fig. 3

The QTL for the KRN identified using the BSR-seq strategy. The posterior probability of each SNP indicates the probability of complete linkage between the SNP and a causal locus for the KRN

Fig. 4

Distribution of the KRN of RILs and the QTL for the KRN detected on chromosome 8 genotype coding method