Characterization of Domestication Loci Associated with Awn Development in Rice

• Published in: Rice (New York, N.Y.) Vol. 15; no. 1; p. 61
• Main Authors: Luong, Ngoc Ha, Balkunde, Sangshetty G., Shim, Kyu-Chan, Adeva, Cheryl, Lee, Hyun-Sook, Kim, Hyun-Jung, Ahn, Sang-Nag
• Format: Journal Article
• Language: English
• Published: New York Springer US 30-11-2022; Springer Nature B.V; SpringerOpen
• Subjects: Agriculture; Annotations; Awn development; Biomedical and Life Sciences; Chromosomes; Cloning; Cultivars; Domestication; Gene mapping; Genes; Genetic control; Haplotypes; Leucine; Leucine zipper proteins; Life Sciences; O. minuta; Plant Breeding/Biotechnology; Plant Ecology; Plant Genetics and Genomics; Plant Sciences; qAwn9; Quantitative trait loci; Rice; Quantitative trait loci; Awn development; Rice
• ISSN: 1939-8425; 1939-8433; 1934-8037
• DOI: 10.1186/s12284-022-00607-y

Rice (
Oryza sativa
L.) is a widely studied domesticated model plant. Seed awning is an unfavorable trait during rice harvesting and processing. Hence, loss of awn was one of the target characters selected during domestication. However, the genetic mechanisms underlying awn development in rice are not well understood. In this study, we analyzed and characterized the genes for awn development using a mapping population derived from a cross between the Korean
indica
cultivar ‘Milyang23’ and a near-isogenic line NIL4/9 derived from a cross between ‘Hwaseong’ and
Oryza minuta
. Two quantitative trait loci (QTLs),
qAwn4
and
qAwn9
, mapped on chromosomes 4 and 9, respectively, increased awn length in an additive manner. Through comparative sequencing analyses of the parental lines,
LABA1
was determined as the causal gene underlying
qAwn4. qAwn9
was mapped to a 199-kb physical region between markers RM24663 and RM24679. Within this interval, 27 annotated genes were identified, and five genes, including a basic leucine zipper transcription factor 76 (
OsbZIP76
), were considered as candidate genes for
qAwn9
based on their functional annotations and sequence variations. Haplotype analysis using the candidate gene revealed tropical-
japonica
specific sequence variants in the
qAwn9
region, which partly explains the non-detection of
qAwn9
in previous studies that used progenies from interspecific crosses. This provides further evidence that
OsbZIP76
is possibly a causal gene for
qAwn9
. The
O. minuta qAwn9
allele was identified as a major QTL, providing an important molecular target for understanding the genetic control of awn development in rice. Our results lay the foundation for further cloning of the awn gene underlying
qAwn9
.