GBS-based SNP map pinpoints the QTL associated with sorghum downy mildew resistance in maize (Zea mays L.)

Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi, threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%–18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs

Incorporation of opaque-2 into ‘UMI 1200’, an elite maize inbred line, through marker-assisted backcross breeding

Maize is an important agricultural plant valued for its productivity and nutritive qualities. However, a deficiency of two essential amino acids (lysine and tryptophan) significantly reduces the nutritional quality of maize proteins. The recessive opaque-2 (o2) mutant has a greater content of lysine and tryptophan in their endosperm proteins and their bioavailability is better. Therefore, marker-assisted backcross breeding (MABB) was attempted to incorporate the o2 allele from the donor line VQL 1 into the genetic background of UMI 1200 to develop quality protein maize (QPM) lines. Foreground selection for the gene o2 was effected using tightly linked molecular marker umc1066, in UMI 1200 × VQL 1 backcross series. Further, background selection was done together with stringent phenotypic selection for agronomic traits, to accelerate recurrent parent phenome recovery. As a result, three advanced QPM maize lines (DBT 4-1-1/25-10/25-10/25-16, DBT 4-1-1/25-10/25-17/25-11 and DBT 4-1-1/25-10/25-17/25-13) carrying the opaque-2 allele in a homozygous state, similar to VQL 1 were developed. The lysine and tryptophan content of these lines ranged from 0.35% to 0.40% and 0.03 to 0.05%, respectively, which is on par with the VQL 1. Background analysis using 250 simple sequence repeats (SSRs) revealed up to 97% recurrent parent genome recovery. In conclusion, the newly developed QPM lines can be used in future maize breeding programmes to improve the nutritional traits