Marker-trait association for low-light intensity tolerance in rice genotypes from Eastern India

Light intensity is a crucial environmental factor that affects photosynthesis and ultimately, grain yield in rice. However, no gene or marker directly associated with improved performance under low-light intensity under field conditions has been identified till date. With an aim of identifying genes and markers associated with improved performance (measured in terms of better yields) under low-light intensity, an integrated field screening, in silico and wet lab validation analysis was performed. Field-based screening of a diverse set of 110 genotypes led to the identification of two physiological and three morphological parameters critical for low-light tolerance in rice. In silico analysis using information available in public databases led to the identification of a set of 90 potential candidate genes which were narrowed to thirteen genic targets for possible marker-trait association. Marker-trait association on the panel of 48 diverse rice genotypes varying in their response to low-light intensity led to the identification of six markers [HvSSR02-44 (biological yield), HvSSR02-52 (spikelet fertility), HvSSR02-54 (grain yield), HvSSR06-56 (spikelet fertility), HvSSR06-69 (spikelet fertility; biological yield), HvSSR09-45 (spikelet fertility)] lying on chromosomes 2, 6 and 9 showing significant association (R² > 0.1) for traits like grain yield/plant, biological yield and spikelet fertility under low light. Eight rice genes [including member of BBX (B-box) family] lying within 10 kb distance of these identified markers already reported for their role in response to stress or change in plant architecture in rice were also identified. The eight rice genotypes, five traits, eight genes and six markers identified in the current study will help in devising strategies to increase yield under low light intensity and pave way for future application in marker-assisted breeding.