Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers

Abstract

Indica-japonica variation represents the most significant genetic differentiation in Asian cultivated rice (Oryza sativa L. subsp. indica Kato or subsp. japonica Kato). Understanding the differentiation and distribution patterns of cultivated rice along altitude gradients will facilitate strategic utilization and conservation of rice germplasm from mountainous regions. In this study, we analyzed 203 varieties and 14 wild accessions of rice collected from localities across an altitude gradient between 450 and 2,350 m above sea level in Yunnan, China, applying the ''InDel molecular index'' developed recently. Results from PCA of the InDel data demonstrated significant genetic differentiation of rice varieties from Yunnan into indica and japonica types. A few cultivars and nearly all wild rice accessions showed only moderate or no differentiation. Further analyses demonstrated a clear distribution pattern of the rice varieties in the mountainous region: indica varieties were grown across the entire altitude gradient in the sampling areas, but most japonica varieties were found above 1,400 m. These results clearly indicated that indica rice could be cultivated in areas at much higher altitudes than those categorized by the traditional methods. The knowledge opens a new dimension for introducing indica rice varieties to mountainous regions at higher altitudes and for selecting rice germplasm in these regions. In addition, the pattern of significant indicajaponica differentiation in rice varieties from Yunnan suggested the exotic origin of cultivated rice, which did not support the hypothesis that Yunnan is a part of the center of origin of rice, although it is certainly one of the centers of genetic diversity for rice.

Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics

“…For example, japonica cultivars are mainly cultivated in temperate environment at high latitudes or altitudes with cool climate conditions, while indica cultivars are usually grown in tropical and subtropical regions at low latitudes or altitudes16. To assess differences in chemical composition between japonica and indica sub-species, we compared their mature seed metabolomes.…”

Genetic diversity in blast resistance of Bhutan rice landraces

“…Our landrace material consisted of only indica type cultivar grown from as low as 115-2,600 m above sea level and such broad zone of adaptation have been reported in indica type landrace in China across altitudinal cline from 450 to 2,350 m above sea level (Xiong 2010). The grouping based on altitude in our study corresponded well with significant differences found in morpho-physiological characters in landraces along altitude cline in 31 rice cultivars and 68 weedy strains (Ishikawa et al 2005), collected from some of the same sites in Bhutan.…”

Past and present dynamics of sorghum and pearl millet diversity in Mount Kenya region

“…Furthermore, crop adaptation to agricultural practices and local conditions, through farmers’ seed selection, is also involved in crop diversity patterns (Mercer et al., ; Pressoir & Berthaud, ). The combination of seed selection and diffusion processes was notably involved in diversity patterns of barley in Ethiopia and rice in Yunnan, where particular landraces were circumscribed to specific elevations (Samberg et al., ; Xiong et al., ). Similar results were also reported for maize in Mexico where genetic differentiation among elevation zones was observed at a regional scale (van Heerwaarden, ), while other studies found that ethnolinguistic differences have a stronger impact than elevation at a local scale (Orozco‐Ramírez et al., ).…”