Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute

Abstract

BackgroundAlthough the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world’s largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs.ResultsFrom the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species.ConclusionsThai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-19) contains supplementary material, which is available to authorized users.

Genetic diversity of rice (Oryza sativa) germplasm from six countries using simple sequence repeats markers

“…They used Indian quality rice germplasm and reported an average of 6.80 alleles per locus. The number of alleles detected in the present study is lower than those observed by Chakhonkaen et al (2012), who reported a total of 127 alleles that ranged from 4 to 12 alleles using 19 InDel (Insertion-Deletion) markers to evaluate genetic diversity in 101 rice accessions. The average genetic diversity of 0.60 obtained was higher compared to 0.55 previously reported by Sajib et al (2012), who used nine SSR markers to study genetic diversity among 12 aromatic landraces of rice.…”

Evaluation of genetic diversity in rice (Oryza sativa and Oryza glaberrima) germplasm from Liberia and Ghana using simple sequence repeat (SSR) markers

“…They used Indian quality rice germplasm and reported an average of 6.80 alleles per locus. The number of alleles detected in the present study is lower than those observed by Chakhonkaen et al (2012), who reported 127 alleles that ranged from 4 to 12 alleles using 19 InDel (Insertion-Deletion) markers to evaluate genetic diversity in 101 rice accessions. In another study, Hossain et al (2012) found an average of 3.8 alleles per locus in rice using Bangladeshi ARLs.…”

“…Plant breeders referenced information on genetic diversity and relatedness in crop germplasm because it assists them in planning crosses (Chakhonkaen et al, 2012). This information is useful in designing strategies used to improve traits, maintain and manage germplasm in Genetic Resource Centres, or enhance the genetic base of future varieties.…”

Comparative study of endophytic and endophytic diazotrophic bacterial communities across rice landraces grown in the highlands of northern Thailand

“…Although the majority of locally cultivated rice landraces are cultivated by traditional or natural rice farming without any chemical inputs and pest controls, they have been able to produce reasonable yields year by year (Oupkaew et al 2011;Parzies et al 2004;Purnomo et al 2005). This traditional cultivation of the rice landraces requires both specific farming practices and unique local conditions (Chakhonkaen et al 2012;Oupkaew et al 2011;Saito et al 2006). Investigations have revealed that genetic diversity of the rice landraces is one of the reasons which enable their evolutionary adaptation and selection to those traditional practices and farming systems (McCouch 2004).…”