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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 F 2  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 F 2  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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3240-y) contains supplementary material, which is available to authorized users.

bmc genomics

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