Low temperature is a major factor limiting rice productivity and geographical distribution. Improved cold tolerance and expanded cultivation to high-altitude or high-latitude regions would help meet growing rice demand. Here we explored a QTL for cold tolerance and cloned the gene, CTB4a (cold tolerance at booting stage), encoding a conserved leucine-rich repeat receptor-like kinase. We show that different CTB4a alleles confer distinct levels of cold tolerance and selection for variation in the CTB4a promoter region has occurred on the basis of environmental temperature. The newly generated cold-tolerant haplotype Tej-Hap-KMXBG was retained by artificial selection during temperate japonica evolution in cold habitats for low-temperature acclimation. Moreover, CTB4a interacts with AtpB, a beta subunit of ATP synthase. Upregulation of CTB4a correlates with increased ATP synthase activity, ATP content, enhanced seed setting and improved yield under cold stress conditions. These findings suggest strategies to improve cold tolerance in crop plants.

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Genetic diversity and geographic distribution of rice landraces in Yunnan, Southwest China were investigated based on 31 morphological traits (including Ding and Cheng's classification traits) using 6,121 accessions, 41 morphological traits and 12 polymorphic isozyme loci within the primary core collection of 912 accessions, and 20 microsatellite markers within the core collection of 692 accessions. Yunnan is the richest center of genetic diversity of rice (O. sativa L.) germplasm in China, in which indica varieties were derived from 108 counties in 16 prefectures and japonica varieties from 99 counties in 17 prefectures. Geographic distribution and diversity of six ecogroups and classification traits displayed clear differences. The average diversity indices of six ecogroups of rice landraces in Yunnan ranked as follows: javanica (1.2319), aman (1.1738), communis (1.1726), nuda (1.1618), aus (1.1371) and boro (0.9889), and the percentages were 3.6%, 43.9%, 32.1%, 18.1%, 2.1% and 0.2%, respectively. Lincang, Simao, Xishuangbanna and Dehong prefectures form the genetic and gene diversity center of rice landraces in Yunnan, especially Lincang Prefecture is not only the main genetic diversity center of rice landraces in Yunnan but also the diversity center of Ding's and Cheng's classification traits. South marginal paddy-upland rice region with Myanmar is the center of the gene diversity of rice landraces in Yunnan. A core collection from Yunnan rice landraces was identified based on morphological, isozyme and DNA variations, which have confirmed that Yunnan is the center of genetic differentiation of indica and japonica subspecies of Asian cultivated rice.

Yunnan Province is one of the largest centers of genetic diversity of Oryza sativa L. in China, and in the world. Using a genetically representative core collection of 692 rice landraces from Yunnan, the genetic structure, differentiation, and geographic diversity of this rice germplasm were analyzed. The accessions were classified into different populations, according to the model-based structure analysis. Model-based populations were characterized through the reconstruction of a neighbor-joining tree, principal coordinate analysis, and the estimation of morphologic and SSR variations. Finally, the distribution of genetic diversity and differentiation among districts were studied. Seven model-based populations were identified on the basis of the structure analysis. This classification was partly consistent with Ting's 5-level taxonomic system. Differentiation between 2 rice subspecies is the most apparent, with a clearer differentiation between soil-watery ecotypes in japonica than in indica; however, differentiation among seasonal ecotypes in indica is clearer than in japonica. Cropping system and man-made restricted-growth environments could be considered to be the main forces driving the intraspecific differentiation of cultivated rice. It has been suggested that, because it possesses the highest genetic diversity and all the necessary conditions as a center of genetic diversity, the southwest region of Yunnan, encompassing Simao, Lincang, and Xishuangbanna districts, is the center of genetic diversity of Yunnan rice landraces.