Identification of Novel Quantitative Trait Loci and Candidate Genes Associated with Grain Yield and Related Traits Under Low-Light Stress Conditions in Rice

TL;DR

This study identifies new genetic regions and genes in rice that help it tolerate low-light conditions, which could improve rice yields in regions with poor light.

Contribution

The study discovers 20 novel QTLs and three key hub genes linked to low-light tolerance in rice.

Findings

33 stable QTLs were identified, with 11 specific to low-light conditions.

Three hotspot regions on chromosomes 1, 4, and 8 were found to contain 10 novel QTLs.

Three key hub genes (OsAUX1, OsSBDCP1, OsNPF5.16) were linked to low-light tolerance.

Abstract

Low light intensity is a major abiotic stress that severely affects rice yields, particularly in India and Southeast Asia, causing yield reductions of 35–40% during the wet season compared to the dry season. Tolerant rice genotypes exhibit adaptive changes at anatomical, physiological, biochemical, and molecular levels under low-light stress, enabling higher yields compared to susceptible varieties. Our study identified 20 novel QTLs associated with grain yields and nine related traits under low-light and control (normal)-light conditions, using a recombinant inbred line (RIL) population derived from the cross between the low-light-tolerant variety Swarnaprabha and the low-light-susceptible variety IR8. Across the Kharif seasons of 2019 and 2021, 33 stable QTLs were identified, with 11, 13, and 9 QTLs specific to low-light, normal-light, and both conditions, respectively. Of these, Swarnaprabha contributed 28 QTLs, while five were contributed by IR8. Notably, the study identified 11 and 9 novel QTLs under low-light and both conditions, respectively. Three hotspot regions on chromosomes 1, 4, and 8 were identified. These regions harbored 10 novel QTLs and revealed twenty candidate genes, out of which three key hub genes, OsAUX1, OsSBDCP1, and OsNPF5.16, were identified. These hub genes are involved in hormone signaling, starch metabolism, and nitrogen metabolism, respectively. A comprehensive expression analysis of these genes indicated that they are linked to low-light tolerance, offering deeper insights into the genetic and molecular mechanisms underlying low-light resilience. These findings provide valuable genomic resources and potential markers for breeding programs for improving rice productivity under low-light conditions.

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