Abstract
Key messageMaize kernel row number might be dominated by a set of large additive or partially dominant loci and several small dominant loci and can be accurately predicted by fewer than 300 top KRN-associated SNPs.Kernel row number (KRN) is an important yield component in maize and directly affects grain yield. In this study, we combined linkage and association mapping to uncover the genetic architecture of maize KRN and to evaluate the phenotypic predictability using these detected loci. A genome-wide association study revealed 31 associated single nucleotide polymorphisms (SNPs) representing 17 genomic loci with an effect in at least one of five individual environments and the best linear unbiased prediction (BLUP) over all environments. Linkage mapping in three F2:3 populations identified 33 KRN quantitative trait loci (QTLs) representing 21 QTLs common to several population/environments. The majority of these common QTLs that displayed a large effect were additive or partially dominant. We found 70 % KRN-associated genomic loci were mapped in KRN QTLs identified in this study, KRN-associated SNP hotspots detected in NAM population and/or previous identified KRN QTL hotspots. Furthermore, the KRN of inbred lines and hybrids could be predicted by the additive effect of the SNPs, which was estimated using inbred lines as a training set. The prediction accuracy using the top KRN-associated tag SNPs was obviously higher than that of the randomly selected SNPs, and approximately 300 top KRN-associated tag SNPs were sufficient for predicting the KRN of the inbred lines and hybrids. The results suggest that the KRN-associated loci and QTLs that were detected in this study show great potential for improving the KRN with genomic selection in maize breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2581-2) contains supplementary material, which is available to authorized users.
Highlights
Maize kernel row number (KRN) per ear is one of the most important yield components and is a breeding goal for the improvement of maize inbred lines
The number of independent tests (Meff) for the 48962 single nucleotide polymorphisms (SNPs) of Panel 1 was 48498.7, similar to total SNPs number. This result was different from the finding of Rincent et al, who found a larger decrease in Meff compared to total SNPs number (2014)
Investigations using segregation populations that were derived from biparental cross, such as RILs, BCn, and DH, frequently identified only few major QTLs (~10 % phenotype variance explained (PVE)) and several minor QTLs due to limited allelic effect differences between the two parents
Summary
Maize kernel row number (KRN) per ear is one of the most important yield components and is a breeding goal for the improvement of maize inbred lines. A better knowledge of the genetic architecture of KRN is required to establish breeding programs. Current knowledge about the genetic control of the maize KRN was mainly obtained from genetic assays of inflorescence mutants. Suppressor of sessile spikelets 1 (Sos1) controls meristem determinacy to produce single instead of paired spikelets in the inflorescence, thereby decreasing the KRN in the ear (Wu et al 2009). The dominant Corngrass (Cg1) mutant encodes two tandem zma-miR156 genes and leads to a small ear lacking an ordered kernel row and unbranched tassel (Chuck et al 2007)
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