Wu B, Yun P, Zhou H, Xia D, Gu Y, Li P, Yao J, Zhou Z, Chen J, Liu R, Cheng S, Zhang H, Zheng Y, Lou G, Chen P, Wan S, Zhou M, Li Y, Gao G, Zhang Q, Li X, Lian X, He Y.

Plant Cell. 2022 Apr 26;34(5):1912-1932. doi: 10.1093/plcell/koac057.

Abstract

Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.

See https://pubmed.ncbi.nlm.nih.gov/35171272/

Figure 2: Map-based cloning of the QTL WCR1 and agronomic traits of the NILs. A, Location of WCR1 (marked in red) in the genetic map. B and C, Fine mapping of the WCR1 region using Population 1 (B) and Population 2 (C). No. of Recs. indicates the number of recombinants between WCR1 and flanking molecular markers. D, Genotypes and phenotypes of recombinants, each of which was confirmed by progeny test (Supplemental Table S1). E, Plant and seed characteristics of the NILs. Scale bars, 10 cm (plants), 10 mm (grains), and 500 µm (transverse sections of brown rice grains). F–I, Comparisons of WCR, head rice yield, 1,000-grain weight, and yield per plant between NIL-WCR1-BL and NIL-WCR1-J. Data are means (n = 30) with error bars, sem. P-values were determined by two-tailed t tests, *P ≤ 0.05, **P ≤ 0.01.