Two SNP Mutations Turned off Seed Shattering in Rice

• Main Authors: Yu Zhang, Jiawu Zhou, Ying Yang, Walid Hassan Elgamal, Peng Xu, Jing Li, Yasser Z. El-Refaee, Suding Hao, Dayun Tao
• Format: Article
• Language: English
• Published: MDPI AG 2019-11-01
• Series: Plants
• Subjects: seed shattering; <i>o. barthii</i>; <i>o. sativa</i>; <i>hs1</i>; haplotype
• Online Access: https://www.mdpi.com/2223-7747/8/11/475

Seed shattering is an important agronomic trait in rice domestication. In this study, using a near-isogenic line (NIL-<i>hs1</i>) from <i>Oryza barthii</i>, we found a hybrid seed shattering phenomenon between the NIL-<i>hs1</i> and its recurrent parent, a <i>japonica</i> variety Yundao 1. The heterozygotes at <i>hybrid shattering 1</i> (<i>HS1</i>) exhibited the shattering phenotype, whereas the homozygotes from both parents conferred the non-shattering. The causal <i>HS1</i> gene for hybrid shattering was located in the region between SSR marker RM17604 and RM8220 on chromosome 4. Sequence verification indicated that <i>HS1</i> was identical to <i>SH4</i>, and <i>HS1</i> 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 <i>SH4</i> 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 <i>HS1</i> 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.