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Evaluation of Genetic Diversity of Rice Landraces (Oryza Sativa L.) in Yunnan, China

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Evaluation of Genetic Diversity of Rice Landraces (Oryza Sativa L.) in Yunnan, China Breeding Science 57 : 91–99 (2007) Evaluation of Genetic Diversity of Rice Landraces (Oryza sativa L.) in Yunnan, China Yawen Zeng*1,2), Hongliang Zhang§3), Zichao Li*3), Shiquan Shen2), Jianli Sun3), Meixing Wang3), Dengqun Liao3), Xia Liu3), Xiangkun Wang3), Fenghui Xiao*1) and Guosong Wen1) 1) Key Laboratory of Agricultural Biodiversity for Plant Disease Management of Ministry of Education, Yunnan Agricultural University, 650201 Kunming, China 2) Biotechnology and Genetic Resources Institute, Yunnan Academy of Agricultural Sciences, 650205 Kunming, China 3) College of Agronomy and Biotechnology, China Agricultural University, 100094 Beijing, China 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 acces- sions, 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 distri- bution and diversity of six ecogroups and classification traits displayed clear differences. The average diver- sity 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 prefec- tures 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 identi- fied 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. Key Words: genetic diversity, core collection, evaluation, distribution, rice landraces, Yunnan. Introduction indica and japonica subspecies are very apparent. Variation in spikelet shape of indica and japonica rice cultivars of Genetic diversity is a ubiquitous property of all species Asian origin, and indica/japonica non-random association in in nature. The ‘Green Revolution’ has remarkably increased characters and genes reflect the independent origin of the crop productivity over the past four decades (Mann 1997). two types from different wild ancestors (Sato 1991, 1996). However, this agricultural transformation has also resulted The indica line of rice varieties evolved from the annual in problems, including the loss of crop genetic diversity gene pool of the AA genome and the japonica varieties from (Tilman 1998). Narrow genetic base in current rice cultivars the perennial gene pool of the AA genome of wild rice continues to limit the productivity of rice which has been (Yamanaka et al. 2003). The O. sativa rice accessions cultivated for more than 9000 years and is a staple food for sampled show a significant differentiation into five groups: over 50% of the human population. However, there is a re- aromatic, aus, indica, temperate japonica and tropical markably high diversity in cultivated rice. Rice landraces es- japonica (Amanda et al. 2005). China is the center of ori- pecially in the core collections from the diversity center are gin and genetic diversity of japonica and O. rufipogon, and important reservoirs of useful genes and can be exploited to one of the two centers of origin of indica rice (Chang 1976, both broaden the existing narrow genetic base and enrich the Oka 1988, Li and Rutger 2000, Li 2001, Gao et al. 2000, existing varieties with important favorable agronomic traits. Zeng et al. 2001b, 2003). At all the levels of analysis, the differences between the Yunnan is the center of genetic diversity of O. sativa in China, and indica-japonica differentiation at the isozyme Communicated by Y. Sato and RFLP levels has been well documented (Nakagahra Received January 27, 2003. Accepted October 30, 2006. 1978, Nagamine 1992, Ise et al. 2000, Li 2001, Zeng et al. § These authors contributed equally to this work 2003). Ise et al. screened 581 varieties from Yunnan (n = *Corresponding author (e-mail: [email protected]) 376) and Japan (n = 205) for the endosperm amylose content, 92 Zeng, Zhang, Li, Shen, Sun, Wang, Liao, Liu, Wang, Xiao and Wen and Yunnan rice showed a 1.7 time larger variation than Jap- cultural Sciences 1986). The statistical methods (diversity anese rice, based on the Shannon-Wiener index (http:// indices, etc.) and 60 characters of 6,121 accessions had been www.jircas.affrc.go.jp/english/publication/news/2000/No.23/ previously described in detail (Zeng et al. 2000a, 2003). 06Ise.htm). Nagamine (1992) suggested that Southwest One hundred plants of each accession from the primary Yunnan is the center of isozyme genetic variation. Yunnan core collection of 912 accessions, which accounted for 98% rice landraces can be divided into 58 variety types, which of the diversity of a total of 6,121 landraces in Yunnan (Zeng correspond to most of the types found in China, and the et al. 2002, http://www.zgzzkj.org, Li et al. 2002) were cultivars account for 8.6% of the total cultivars in China grown in five rows in a field of the experimental farm locat- (Zeng et al. 2003). It was revealed that Yunnan is the richest ed in Xingping county (500 m asl). Mid-maturity rice was center of genetic and gene diversity of O. sativa among the planted in the summer of 1999. The morphological diversity 29 provinces of China, based on the analysis of the genetic and genetic differentiation index of 41 traits (18 qualitative diversity distribution of China rice cultivars at the provincial and 23 quantitative traits) among the 5 ecological zones or 17 level, using 26 phenotypic characters of 50,526 accessions prefectures were calculated by the following two formulas from China rice germplasm collections, nine polymorphic using Foxpro software and the VB system: I = −ΣPijLogPij , th th isozyme loci from the core collection of 5,181 accessions, where Pij is the frequency of the j phenotype of the i and 36 microsatellite markers from the core collection of character, and I is the genetic diversity index (King et al. 4,300 accessions (Li 2001, Zhang et al. 2007). The present 1989); Dr = (It − Ia)/It or Dr = (CVt − CVa)/CVt, where Dr is the study on the diversity of rice landraces in Yunnan will sup- differentiation coefficient of morphological characters be- ply a basis for further investigations on the genetic diversity tween populations, It is the total genetic diversity index, Ia is of rice landraces in China and the world as well as for a bet- the average diversity index, CVt is the total diversity index ter utilization, conservation and management of O. sativa. for a certain character, and CVa is the average diversity index resources. for a certain character between populations (Nei 1977). Gene diversity index and coefficient of genetic differ- Materials and Methods entiation of 912 accessions and 692 accessions from core collections among ecological zones and subspecies were es- A total of 6,121 accessions of rice landraces with 60 char- timated, respectively, using 12 isozyme loci and 20 pairs of acters defined and evaluated were collected from the Seed SSRs. The gene diversity index was expressed as follows: H 2 Bank of the Yunnan Academy of Agricultural Sciences, = 1 − ΣPij /N, where N is the number of loci, and Pij is the fre- covering 109 counties in 17 prefectures in Yunnan, China. quency of the ith allele at the jth locus (Nei 1973). The coeffi- In order to characterize and evaluate the related traits, all cient of genetic differentiation was as follows: Gst = (Ht − Ha)/ the 912 accessions of Yunnan rice landraces were sowed in Ht, where Ht corresponds to the total gene diversity indices the middle season of rice cultivated (e.g. June 29 in 1999) in within populations, Ha is the average gene diversity index Xinping county, Yunnan (550 m above the sea level). The for each population (Nei 1977). The detection methods of subspecies (indica or japonica) and ecogroups (javanica, isozyme and SSR polymorphisms were described separately nuda, communis, aus, aman and boro) were classified ac- by Li et al. (2001), Oka (1988) and Temnykh et al. (2000). cording to the method of Cheng (1993) and Zeng et al. Twelve isozyme loci included Est-1 (0, 1, 2, 3), Est-2 (0, 1, (2001a). Indica was classified into boro, aus and aman, 2), Est-10 (0, 1, 2, 3, 4), Cat-1 (1, 2), Amp-2 (1, 2), Acp-2 (0, which boro and aus were mainly distributed below the ele- x, 1), Acp-1 (y, 1, 2), Mal-1 (1, 2), Mal-3 (y, 1, 2), Mal-x (1, vation of 800 m, but aman below the elevation of 1,200 m. 2), Pgd-1 (1, 2, 3) and Pg-2 (1, 2). Twenty SSR primers with Boro heads during the period of 5–12 September, aus before a high polymorphism that were allocated to 12 chromo- September 10 and aman after September 10. Generally somes included RM5, RM81A, RM263, RM211, RM60, speaking, japonica rice were mainly distributed over the el- RM232, RM255, RM241, RM249, RM225, RM253, RM18, evation of 1,850 m, but japonica varieties distributed below RM234, RM223, RM257, RM258, RM244, RM224, the elevation of 1000 m were javanica.
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