Association mapping for yield traits under drought stress in Autumn rice germplasm collection of Assam

Association mapping approach was applied to identify regions linked to SSR markers with yield and related traits in drought stress conditions using 267 autumn rice germplasm collection of Assam. The germplasm exhibited extensive phenotypic and genotypic diversity in both irrigated and artificial drought stress conditions. The drought screening in rainout shelter was successful causing a reduction of mean yield up to 65% in contrast to irrigated conditions. The grain yield showed a positive correlation with traits like productive tiller number, spikelet fertility, and relative leaf water content in drought stress situations suggesting their scope for use as an indirect selection parameter in breeding autumn rice. Many traditional autumn genotypes like ‘Koni ahu’, ‘Garam ahu 2’, ‘Bengonagutiya’, ‘Ahu Joha’ were found to be tolerant in drought stress conditions. The population structure study revealed the presence of structure in the panel dividing 203 accessions into two subgroups and leaving sixty-nine accessions under admixed ancestry. The marker-trait association (MTA) studies using structured mixed linear model (MLM) method unveiled 64 MTA for nine different traits under drought stress conditions. For grain yield, six MTA’s were reported on chromosome 2, 3, 5, 6 and 10 explaining the Phenotypic Variance in the range of 6 to 16%. Seven novel MTA were obtained for their corresponding traits and many of the identified QTL’s were reported previously. Some of the associations were also consistent with General linear model study. Candidate gene analysis of associated marker regions inferred that there are certain stress-responsive genes in its proximity. The tolerant genotypes identified can be employed in different drought breeding programs. The novel associations with major effect offer scope in the mining of new alleles for traits associated with drought tolerance for this class of rice.