Rice Genomics and Genetics 2024, Vol.15, No.2, 83-93 http://cropscipublisher.com/index.php/rgg 90 The Bashidang site, located in the middle reaches of the Yangtze River, provides microfossil evidence indicating that early Holocene groundwater fluctuations had a significant impact on rice domestication. The area evolved from a floodplain to a wetland, which facilitated rice domestication through practices of burning and clearing. However, due to rising groundwater levels, rice cultivation ceased around 8 00~7 900 years ago (Fuller et al., 2009; Ma et al., 2018). Phytolith evidence from Diaotonghuan Cave in northern Jiangxi supports the hypothesis that the middle reaches of the Yangtze River were one of the centers of rice domestication. This evidence aligns with the broader understanding that domesticated rice first appeared in the Yangtze River basin. A comprehensive study of 38 archaeological samples from eight Neolithic sites in the lower Yangtze region suggests that the rice domestication process lasted approximately 6 000 years and can be divided into three stages (Ma et al., 2016). The study highlights the gradual and continuous development of domesticated rice traits, with significant turning points during the middle Hemudu culture, late Majiabang culture, and late Liangzhu culture periods (Liu et al., 2017). Evidence from the early Neolithic Shishan site suggests that barnyard grass was a major staple alongside rice. This indicates that early managed wetland environments were initially harvested for multiple grain varieties, and the emergence of rice as a favored cultivated grass was a prolonged process. These case studies collectively illustrate the gradual and multifaceted nature of rice domestication in the Yangtze River basin, influenced by environmental changes and human agricultural practices. The transition from wild to domesticated rice involved different stages and strategies, reflecting the complex interplay between natural and cultural factors (Cheng et al., 2019). 6 Key Archaeological Sites and Their Role in Understanding Rice Domestication The domestication of rice has been extensively studied, with significant contributions from archaeological sites across Asia, providing crucial insights into the geographical and temporal aspects of rice domestication. One of the key regions identified is the area south of the Himalayas, encompassing eastern India, Myanmar, and Thailand (Huang et al., 2012). This region is considered a domestication center for one of the major rice varieties, indica (Oryza sativa subsp. Indica). Archaeological evidence from these areas supports the hypothesis of independent domestication events, highlighting the role of local wild rice populations in the development of cultivated rice. Southern China, particularly the central region of the Pearl River, has also been identified as a significant location for rice domestication. Archaeological findings indicate that japonica rice was first domesticated from specific populations of wild rice ancestors (Oryza rufipogon) in this region. Following this domestication event, japonica rice spread to Southeast and South Asia, where it further hybridized with local wild rice populations, contributing to the genetic diversity of modern rice varieties (Zhu et al., 2007). The domestication of rice involved significant genetic changes, which have been elucidated through various genomic studies. One major finding is the identification of selective sweeps, which are genomic regions that underwent strong selection during domestication. A comprehensive map of rice genome variation has revealed 55 such selective sweeps, providing insights into the genetic basis of domestication-related traits (Zhang et al., 2016). Comparative genomic analyses between wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa) have shown a drastic reduction in nucleotide diversity in the latter. This reduction indicates the presence of a severe domestication bottleneck, with only a small fraction of the genetic diversity in wild rice being retained in cultivated rice. It is estimated that the ancestral population of cultivated rice consisted of approximately 1,500 individuals, and the domestication process spanned about 3 000 years (Eizenga et al., 2017). Further research has identified specific genes lost or gained during domestication. For example, structural variations between Dongxiang wild rice and the cultivated Nipponbare variety highlight the deletion or addition
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