Marker–Trait Association for Protein Content among Maize Wild Accessions and Coix Using SSR Markers

Teosinte is the closest wild ancestor of maize and is used as a valuable resource for taxonomical, evolutionary and genetic architectural studies of maize. Teosinte is also a repository of numerous diverse alleles for complex traits, including nutritional value and stress adaptation. Accessions including teosintes, maize inbred lines and coix were investigated for kernel protein and its association with DNA markers. The proposed investigation assumed that wild accessions had different genic/allelic content and consequently expression profile than modern maize because of the domestication syndrome and bottleneck effects. Total protein content in hard stony fruit case teosinte accessions were assessed from kernels with and without seed coats, while protein content from coix and maize lines was evaluated from kernels only. The accessions were also subjected to molecular profiling using 84 SSR markers, and obtained genotypic data were used for population structure and association analysis. The results emphasize that teosintes have higher protein content (18.5% to 26.29%), followed by coix (18.26%), and the least among maize lines (9% to 11%). Among teosintes, without-seed-coat samples had 3–6% higher protein content than with-seed-coat samples. When compared to other teosinte species, <i>Z. mays</i> subsp. <i>mexicana</i> accessions showed higher protein content, ranging from 18.62% to 26.29%. All evaluated accessions were divided into four subpopulations with K = 4, and seven significant (<i>p</i> < 0.01) marker–trait associations were seen with umc1294, umc1171, phi091, umc2182 and bnlg292 markers, which are distributed across chromosomes 4, 5, 7, 8 and 9, respectively. We have observed that the wild relatives carry protein content-enhancing alleles and can be used as productive donor parents in pre-breeding efforts to increase the protein content of maize.