Fine mapping of a major QTL, qECQ8, for rice taste quality

Background: Rice ECQ (eating and cooking quality) is an important determinant of rice consumption and market expansion. Therefore, improvement of ECQ is one of the primary goals in rice breeding. However, ECQ-related quantitative trait loci (QTL) have not yet been fully revealed. The present study aimed to identify a major effect QTL for rice taste, an important component of ECQ via genotyping-by-sequencing, to reveal the associated molecular mechanisms, and to predict key candidate genes.

Results: A population of F₉ recombinant inbred lines resulting from a cross between R668 (national standard of high-quality third class) and R838 (common edible rice) was used to construct a high-density genetic map (2,295.062 cM). The map comprises 639,504 markers distributed on 12 linkage elements with an average genetic distance of 0.004 cM. We detected a major taste-related QTL, qECQ8, which explained 41.4% of phenotypic variance and had LOD values of 4.42-7.73. Using a five-generation NIL population from the backcross of "Ganxiangzhan No. 1" carrying qECQ8 with the recurrent parent R838 (without qECQ8), we narrowed qECQ8 to a 187.5 kb interval between markers M33 and M37 on Chr8. Comparative transcriptomic analysis revealed that photosynthesis, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, and alpha-linolenic acid metabolism were induced in developing seeds of lines containing qECQ8. Furthermore, we identified two candidate genes in the qECQ8 region, including LOC_Os08g30550 (zinc knuckle family protein), a major candidate for genetic-assisted breeding of high-quality rice.

Conclusion: Our findings provide important genetic resources for targeted improvement of rice taste quality and may facilitate the genetic breeding of rice ECQ.