Updates and perspectives on the utilization of molecular makers of complex traits in rice

Abstract

ABSTRACT. After complete sequencing of its genome and annotation of the majority of its ~32,000 genes, rice genome has become the model genome among the cereal genomes, and the focus has shifted from structural to functional genomics and application of genomicderived information in rice breeding. During the past 2 decades, intensive worldwide efforts have led to significant improvements in rice. An abundance of molecular markers and information related to many genes/quantitative trait loci that control agronomically important traits such as yield, quality, and biotic and abiotic stress tolerance have been identified. Bridging the application gap between quantitative trait locus identification and marker-assisted selection breeding is an urgent, arduous, and long-term task. Marker development, allele mining, gene discovery, and molecular breeding have progressed to a great extent because of the rapid development of next-generation sequencing, largescale high-density genotyping, and genome-wide selection strategies. The availability of high-density markers and the rapidly decreasing cost of genotyping have facilitated marker-assisted selection of many traits that were previously not possible.

Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding

“…Compared to conventional breeding, DNA polymorphism based marker-assisted selection (MAS) is more reliable and efficient, providing better selection strategies [ 9 , 10 ] which can accurately select target genes in early generations and avoid the transfer of undesirable or deleterious genes. Recently, many rice varieties have been selected based on the MAS strategy [ 11 – 14 ], which opens up a new prospect for genetic improvement in rice.…”

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).…”