Analysis of Genetic Diversity and Relationships in Waxy Rice (Oryza sativa L.) using AFLP and ISSR Markers

Abstract

Opaque endosperm is the main phenotypic indicator for waxy rice, but other phenotypic and genotypic variation among waxy rice accessions has largely been ignored. Previous studies showed that wide diversity in starch physiochemical properties exists in both indica and japonica waxy rices, especially for starch gelatinization temperature (GT) which could be divided into a high-and a low-GT group. In the present study, amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) molecular markers were employed to examine genetic diversity and relationships of 56 waxy rice accessions. A total of 358 AFLP fragments were amplified with five primer combinations, showing a high level of polymorphism (78.3%). A total of 190 ISSR bands were generated with a single primer and a primer pair, showing a very high level of polymorphism (92.2%). The genetic distance matrices obtained from the two sets of markers were significantly correlated (r ¼ 0.731, P ¼ 0.004). The dendrogram generated with combined AFLP and ISSR markers could clearly differentiate the indica and japonica groups. Newly released varieties and breeding lines within each subspecies tended to be clustered together, whereas landraces were more distantly placed in the dendrogram. Only one AFLP band was found specific to the indica type, while no specific bands were found for starch GT. The implications for the conservation and breeding of waxy rice are discussed.

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)

“…Among these qualitative properties, consumers pay most attention to fine appearance and high eating quality (Huang et al, 1998;Zhao et al, 2012b). AC is related to the appearance and texture of rice, and it affects cooking and eating quality (Bao et al, 2006;Lu and Park, 2012). Hence, regulating the AC in rice has been a major concern of rice breeders.…”

“…In contrast to morphological traits, molecular markers can reveal differences among genotypes based on DNA polymorphisms, providing a direct, reliable, and efficient tool for germplasm characterization, conservation, and management. Many DNA markers have been developed and have become powerful tools for detecting the GD within and between populations, including restriction fragment length polymorphisms (Sun et al, 2001), amplified fragment length polymorphisms (Bao et al, 2006), random amplified polymorphic DNA (Rabbani et al, 1998), sequence-characterized amplified regions (Li and Park, 2012), simple sequence repeats (SSRs) (Giarrocco et al, 2007), and single nucleotide polymorphisms (McNally et al, 2009). SSRs are the markers of choice for crop improvement in many species because they are reliable and easy to score (Gupta and Varshney, 2000;Moe and Park, 2012).…”

Evaluation of Genetic Structure of Amaranth Accessions from the United States

“…Many molecular markers have been used to analyze diversity, such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and single nucleotide polymorphisms (SNPs; Bao et al, 2006;Cheng et al, 2011;Feltus et al, 2004;Jin et al, 2010;Li et al, 2012;Liang et al, 1994;Nagaraju et al, 2002;Zhao et al, 2009). Different marker systems have been used to investigate genetic diversity (Tam et al, 2005), and random amplified polymorphic DNA (RAPD) markers and SSRs have been applied to study the genetic diversity and phylogenetic relationships among Amaranthus species (Khaing et al, 2013;Lee et al, 2008;Wassom and Tranel, 2005;Xu and Sun, 2001).…”

Analysis of the Genetic Diversity and Population Structure of Amaranth Accessions from South America Using 14 SSR Markers

“…Due to the agro-economic importance of amaranths, several studies of isozymes and various DNA markers have been performed to understand intra-and interspecific genetic diversity and/or evolutionary relationships (Lanoue et al, 1996;Chan and Sun, 1997;Sun et al, 1999). Several valuable methods for molecular marker systems, such as restriction-fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD), sequencetagged sites (STS), amplified fragment length polymorphisms (AFLP), simple sequence repeats (SSRs) or microsatellites, and single nucleotide polymorphisms (SNPs), have been developed and applied for estimation of genetic diversity (Suh et al, 1997;Nagaraju et al, 2002;Feltus et al, 2004;Bao et al, 2006;Zhao et al, 2009;Li et al 2012). Various marker systems have been used specifically to investigate genetic diversity (Tam et al, 2005).…”