Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.

/pdf/genomic-variation-in-3-010-diverse-accessions-of-asian-41xmvlht7z.pdf

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

Plant domestication is an outstanding example of plant–animal co-evolution and is a far richer model for studying evolution than is generally appreciated. There have been numerous studies to identify genes associated with domestication, and archaeological work has provided a clear understanding of the dynamics of human cultivation practices during the Neolithic period. Together, these have provided a better understanding of the selective pressures that accompany crop domestication, and they demonstrate that a synthesis from the twin vantage points of genetics and archaeology can expand our understanding of the nature of evolutionary selection that accompanies domestication.

/pdf/the-nature-of-selection-during-plant-domestication-51l7jssca2.pdf

The nature of selection during plant domestication

Objectives To summarise evidence on the association between white rice consumption and risk of type 2 diabetes and to quantify the potential dose-response relation.

/pdf/white-rice-consumption-and-risk-of-type-2-diabetes-meta-3frw87p965.pdf

White rice consumption and risk of type 2 diabetes: meta-analysis and systematic review

https://www.ndsu.edu/pubweb/~mcclean/plsc731/homework/papers/kovach%20et%20al.%20-%20new%20insights%20into%20the%20history%20of%20rice%20domestication.pdf

New insights into the history of rice domestication

Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice, indica and japonica, were domesticated from the wild rice O. rufipogon. In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between indica and japonica as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200–13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.

https://www.pnas.org/content/pnas/108/20/8351.full.pdf

Molecular evidence for a single evolutionary origin of domesticated rice

This paper is a response, both to Fuller et al.'s recent criticism of Chinese research on rice domestication, as lacking evidence, and to their argument for the beginning of rice domestication around 4000 BC in the lower Yangzi River. We first survey previous publications that discuss the process from wild rice collection to rice domestication in China, and then examine early rice remains from the perspectives of rice morphology and archaeological context. We focus on three aspects: the timing of the initial rice domestication in the Yangzi River region; the earliest presence of domesticated rice in the Lower Yangzi and Huai River regions; and the implications of changes in rice grain sizes in archaeological assemblages. We also discuss problems relating to the presence of immature rice remains in the archaeological record, grain size increase and overall grain shape, which are three of the criteria used by Fuller et al. for distinguishing domesticated from wild rice. Based on published data and our research on rice, we demonstrate that by the early Holocene (9000 cal. BP), Neolithic people in both north and south China may have been harvesting wild rice and initiating rice cultivation that eventually led to domestication.

Evidence for the early beginning (c. 9000 cal. BP) of rice domestication in China: a response

A newly discovered site at Shangshan in the Lower Yangzi River region has revealed the oldest open-air sedentary village and domesticated rice in south China.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0003598X00093674

New evidence for the origins of sedentism and rice domestication in the Lower Yangzi River, China

The discovery of an 8000-year old dugout canoe at Kuahuqiao in the Lower Yangzi River, China.

The earliest rice domestication in China.

Significance We studied goose bones from Tianluoshan—a 7,000-y-old rice cultivation village in the lower Yangtze River valley, China—using histological, geochemical, biochemical, and morphological approaches. Our analyses reveal an early stage of goose domestication at Tianluoshan. The goose population seemed to have been maintained for several generations without the introduction of individuals from other populations and might have been fed cultivated paddy rice. These findings indicate that goose domestication dates back 7,000 y, making geese the oldest domesticated poultry species in history.

Leping. Jiang

Papers

Evidence for the early beginning (c. 9000 cal. BP) of rice domestication in China: a response

New evidence for the origins of sedentism and rice domestication in the Lower Yangzi River, China

The discovery of an 8000-year old dugout canoe at Kuahuqiao in the Lower Yangzi River, China.

The earliest rice domestication in China.

Multiple lines of evidence of early goose domestication in a 7,000-y-old rice cultivation village in the lower Yangtze River, China