Dissection of maize kernel composition and starch production by candidate gene association

Abstract

Cereal starch production forms the basis of subsistence for much of the world's human and domesticated animal populations. Starch concentration and composition in the maize (Zea mays ssp mays) kernel are complex traits controlled by many genes. In this study, an association approach was used to evaluate six maize candidate genes involved in kernel starch biosynthesis: amylose extender1 (ae1), brittle endosperm2 (bt2), shrunken1 (sh1), sh2, sugary1, and waxy1. Major kernel composition traits, such as protein, oil, and starch concentration, were assessed as well as important starch composition quality traits, including pasting properties and amylose levels. Overall, bt2, sh1, and sh2 showed significant associations for kernel composition traits, whereas ae1 and sh2 showed significant associations for starch pasting properties. ae1 and sh1 both associated with amylose levels. Additionally, haplotype analysis of sh2 suggested this gene is involved in starch viscosity properties and amylose content. Despite starch concentration being only moderately heritable for this particular panel of diverse maize inbreds, high resolution was achieved when evaluating these starch candidate genes, and diverse alleles for breeding and further molecular analysis were identified.

Figure 1.

LD Plots of Squared Correlations of Allele Frequencies (r²) against Distance between Polymorphic Sites for the Six Candidate Genes. The lines indicate average r² for 500-bp windows for polymorphisms with a minimum frequency of 0.10. The ae1 graph is based on 1000-bp windows because there were so few polymorphisms per window.

Figure 2.

Genetic Structure of ae1 Sequenced from 32 Maize Taxa. The gene area outlined with a box denotes the region sampled in the full set of 102 taxa. Sites significant for starch pasting factor three (#) and amylose (*) are highlighted. Allele Ae1-1509G associated with higher pasting temperatures in both the summer^C and winter^H replications ([A] and [B]). Allele Ae1-1689 associated with higher amylose in both summer^C and winter^H replications. Insets show the distribution of the data: the median for the data points is marked by the middle horizontal line; the upper and lower horizontal lines highlight the 10th and 90th percentiles. Figures for genes bt2, sh1, and sh2 are set up in the same fashion. Note that the diagonal lines (//) in the gene picture are intronic areas and exon 15 not sequenced in the initial 32 lines.

Figure 3.

Genetic Structure of bt2 with the Significant Region Associated with Kernel Composition Factor Two for Oil. The last exon of bt2 (exon nine) was not sequenced. Diagonal lines near position 3000 (//) denote an area not sequenced because of a highly repetitive 250-bp stretch.

Figure 4.

Genetic Structure of sh1 and the Region Significantly Associated with Kernel Composition Factor Three for G × E Effects and for Amylose Content. The black, unfilled exon denotes noncoding exon one of sh1.

Figure 5.

Genetic Structure of sh2 and the Region Significantly Associated with Kernel Composition Factor Three for G × E Effects and with Starch Pasting Factor One for Multiple Viscosity Traits. Only the trait peak viscosity is shown for space conservation for the allelic distribution of the data.

Figure 6.

sh2 Haplotype Network. Sequencing of a 500-bp region of sh2 revealed six major haplotypes, with haplotype C being the most common with 54 member lines. The least squares mean for amylose content (both winter^H and summer^C replications) and kernel composition factor three (the G × E factor) are reported for each haplotype, signifying the haplotype's average effect on these traits. Major polymorphisms of interest and in LD occurring outside the analyzed region of sh2 are indicated along the branches where the mutations likely occurred.