A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Rice (Oryza sativa L.) is consumed by more than half of the world’s population, but despite its global importance the mechanisms of domestication remain unclear. During domestication, wild rice (O. rufipogon Griff.) was transformed by acquiring non-seed-shattering behaviour, an important genetic change that allowed humans to increase grain yield. However, we show previously identified loci, sh4 and qSH3, are individually insufficient to explain loss of seed shattering nor increases in harvest yield in wild rice. We identify the complementary interaction of key mutations for abscission layer interruption and panicle architecture that were causal in the early domestication of Asian rice. An interruption of abscission layer formation requires both sh4 and qSH3, which presents an apparent barrier to selection of shattering loss. We identified the causal single nucleotide polymorphism at qSH3 within a seed-shattering gene OsSh1 conserved in indica and japonica subspecies, but absent in the circum-aus group of rice. We demonstrate through harvest experiments that seed-shattering alone does not significantly impact yield. Instead, we observed yield increases under a SRR3-controlled closed panicle formation, which is augmented by the integration of sh4 and qSH3 alleles causing a slight inhibition of abscission layer. Complementary manipulation of seed shattering and panicle shape result in a panicle structure that is mechanically stable. We propose a stepwise route in the earliest phase of rice domestication in which selection for visible SRR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3 and leading to loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 is insufficient on its own to cause abscission layer disruption and other genes, such as qSH3 are required, making mechanisms for the initial selection of non-shattering unclear. We show that shattering loss in wild rice genetic backgrounds does not increase yields. We identify an interaction in which a second trait, closed panicle formation controlled by SPR3, both increases yield and facilitates recruitment of sh4 and qSH3 which synergistically augment yield, leading to a stepwise route for rice domestication.

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.

PEMULIAAN DEWI SRI DALAM AKTIVITAS DOMESTIKASI PADI DI BALI

The Balinese agricultural culture has existed since prehistoric times, with the advent of agriculture, especially rice domestication, as an important cultivation to date, gave rise to the myth of Dewi Sri. This study aims to studying the breeding of Dewi Sri in rice domestication activities in Bali, whose data sources were collected through field observations by observing archaeological remains in the form of worship media, lontar manuscripts and inscriptions. Besides being complemented by literature studies of various relevant journals, book and reports. This research has succeeded in revealing that the breeding of Dewi Sri in Bali is very unique, it can be seen from her mention of her local name, the worship media and its symbols are also influenced by Balinese local wisdom. Breeding is also carried out with prayers and ceremonies that are balanced with maintaining and caring for rice and rice field in order to achieve maximum results. Budaya agraris masyarakat Bali telah ada sejak masa prasejarah, dengan munculnya pertanian domestikasi padi sebagai budidaya penting hingga saat ini, memunculkan mitos Dewi Sri. Penelitian ini bertujuan untuk mengkaji pemuliaan Dewi Sri dalam aktivitas domestikasi padi di Bali, yang sumber datanya dikumpulkan melalui observasi di lapangan dengan mengamati tinggalan arkeologi berupa media pemujaan, manuskrip lontar dan prasasti. Selain itu dilengkapi dengan studi pustaka terhadap berbagai jurnal, buku dan laporan yang relevan. Penelitian ini berhasil mengungkap bahwa pemuliaan Dewi Sri di Bali sangat unik dapat dilihat dari penyebutan Dewi Sri dengan nama lokal, media pemujaan dan simbol-simbolnya juga dipengaruhi oleh kearifan lokal Bali. Pemuliaan juga dilakukan dengan doa dan upacara, diseimbangkan dengan memelihara dan merawat padi dan lahan persawahan, agar dapat mencapai hasil yang maksimal.

The identification of grain size genes by RapMap reveals directional selection during rice domestication

Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.

StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication

The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization amongst genes family members in terms of preferential expression across various developmental stages and anatomical parts, such as flowering. Ka/Ks ratios confirmed strong negative/purifying selection on START family evolution, implying that ontogeny recapitulated selection pressures during rice domestication. Our findings provide evidence for high conservation of START genes across rice varieties in numbers, as well as in their stringent regulation of Ka/Ks ratio, and showed strong functional dependency of plants on START proteins for their growth and reproductive development. We believe that our findings advance the limited knowledge about plant START domain diversity and evolution, and pave the way for more detailed assessment of individual structural classes of START proteins among plants and their domain specific substrate preferences, to complement existing studies in animals and yeast.

Ritual Domestikasi Padi Lokal dalam Budaya Sasak-Lombok

The rice plant for Indonesia, especially in Lombok, is considered unique, not only as a production crop but also as a sacred plant. From the process of planting to harvesting, this plant is treated specially with rituals with religious nuances. This study aims to describe the socio-cultural symptoms of local rice domestication rituals among traditional farmers in Lombok. Based on this description, it is hoped that the views, knowledge, values, and rules will become the reference for the behavior of the rural Sasak people as growers of local rice types. The approach used to achieve this goal is a phenomenological approach. Primary data of this study were obtained through in-depth interviews (structured and non-structured to informants) and participatory observation. The results showed that the local rice domestication ritual is a form of awareness of the cultural-religious views of the local community by combining local knowledge and religious knowledge (Sufistic teachings, as represented in the mantra of planting rice and the concept of pare anak iwoq or orphan rice in pare pemol or rice starter/marker) as a manifestation of the awareness of the Supreme Being and the cosmos. This awareness of the Supreme Being and the universe becomes a reference for local farmers in their behavior, especially in agriculture. With these two types of consciousness, they are guided and directed toward safety, security, and balance.