Two SNP Mutations Turned off Seed Shattering in Rice

Abstract

Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-hs1) from Oryza barthii, we found a hybrid seed shattering phenomenon between the NIL-hs1 and its recurrent parent, a japonica variety Yundao 1. The heterozygotes at hybrid shattering 1 (HS1) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal HS1 gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that HS1 was identical to SH4, and HS1 controlled the hybrid shattering due to harboring the ancestral haplotype, the G allele at G237T site and C allele at C760T site from each parent. Comparative analysis at SH4 showed that all the accessions containing ancestral haplotype, including 78 wild relatives of rice and 8 African cultivated rice, had the shattering phenotype, whereas all the accessions with either of the homozygous domestic haplotypes at one of the two sites, including 17 wild relatives of rice, 111 African cultivated rice and 65 Asian cultivated rice, showed the non-shattering phenotype. Dominant complementation of the G allele at G237T site and the C allele at C760T site in HS1 led to a hybrid shattering phenotype. These results help to shed light on the nature of seed shattering in rice during domestication and improve the moderate shattering varieties adapted to mechanized harvest.

Architecture of paleas and lemmas dominates seed shattering trait in naked oat (Avena nuda)

“…There are evidences indicating diverse seed shattering locations governed by different orthologous loci: (Li and Gill 2006). However, no orthologs of Br1 or Br2 were detected in rice, which further confirmed this thesis, as the disarticulation events occurred at the AZ below the florets, governed by qSH1, sh4, SNB, SH5 and other related genes in rice (Di Vittori et al 2019;Maity et al 2021;Dong and Wang 2015;Li and Olsen 2016;Jiang et al 2019a;Zhang et al 2019;Yoon et al 2014). In naked oat, seed shattering relies on the disarticulation of the AZ between seeds and hulls, which is different from all the cases in other reports.…”

“…The development of AZ and the lignin deposition at this section was known to be decisive on seed shattering (He et al 2021;Jiang et al 2019a;Yoon et al 2015;Yoon et al 2017). The genetic control of seed shattering was well studied in rice, and at least two major genes, qSH1 and SH4, have been found to condition rice seed shattering through regulating AZ development (Di Vittori et al 2019;Dong and Wang 2015;Li and Olse 2016;Maity et al 2021;Zhang et al 2019). Other genes such as SH5 and SSH1/SNB are also believed to have large influences on seed shattering by interacting with qSH1 (Jiang et al 2019a;Yoon et al 2014).…”

Analysis of Domestication Loci in Wild Rice Populations

“…This study shows a substantial number of SNPs in the wild populations for these two loci. The two Asian subspecies ( japonica and indica ) have a lower level of genetic variation in terms of the nucleotide diversity at both loci than that found in their wild progenitors [ 38 ]. This study reveals a functional mutation T273G in O. meridionalis exhibiting a wild allele of shattering locus SH4 (orthologs to SHA1 ), which results in an amino acid change from lysine to asparagine at position +79.…”

A Genetic Resource for Rice Improvement：introgression Library of Agronomic Traits for All AA Genome Species in Genus Oryza

“…Since the background of introgression lines is similar to the recurrent parent and it is easier to correlate a particular chromosomal region to phenotypic variation, they were used for mapping and cloning QTLs or genes for complex traits. Many QTLs or genes have been mapped based on introgression lines, such as GS2 for grain size and weight (Hu et al 2015), GL7 for grain size (Wang et al 2015), DEP1 for dense and erect panicle (Huang et al 2009), GS3 for grain length and weight (Fan et al 2006), qPGWC-7 for grain chalkiness (Zhou et al 2009), QTLs for heterosis (Tao et al 2016 (Zhang et al 2019). In this study, 41 loci for grain length, 44 loci for grain width on 12 chromosomes, 42 loci for the ratio of grain length to grain width were explored on 12 chromosomes (Figure 4-6) , and some loci were identi ed in the same location with published genes, such as GW2 (Song et al 2007 In addition, 29 loci might be new QTLs or genes controlled for grain size from the different AA genome donors, and most of published genes for grain size were found based on the introgression library.…”