Genomics of crop plant genetic resources

Abstract

Plant genetic resources collection and utilization had made a huge impact in balancing the genetic diversity of the existing crop plant species and their application in genome based studies had also increased widely. Primarily studies were based on model species, although it now enhances the transferability of information to crops and related species. With the tremendous outbreak of new high-throughput technologies like next-generation sequencing (NGS) and reduction in their costs are bringing many more plants within the range of genome and transcriptome level analysis. The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the crop plant genetic resources to accelerate crop improvement. The future of crop improvement will be centred on comparisons of individual crop plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here I review the importance of crop plant genetic resources and insights that have been emerged in recent years.

Genomic and transcriptomic approaches towards the genetic improvement of an underutilised crops: The case of Bambara groundnut

“…Comparative genomics has been widely used in modern day research as it can provide important information about species whose genomes have not been sequenced by comparing with a known species (Dhanapal, 2012). Rapid advancement in crop genomics has provided a chance to conduct detailed functional and structural comparisons of genes involved in various biological processes among major crops and other plant species.…”

Biodiversity, Genetic Diversity, and Genetic Resources of Date Palm

“…Crop evolution under domestication generally has led to increased productivity and adaptation of crop species, but narrowed their genetic basis (Dhanapal 2012 ;Goldschmidt 2013 ). Date palm evolved under domestication in a manner unlike most other fruit trees, especially those growing under its canopies in oasis agroecosystems.…”

“…Several measures are available to quantify genetic diversity within plant populations; these include, but are not limited to, the amount of polymorphism within populations, the allelic richness (i.e., the total number of alleles in the population), and the gene diversity or probability that two random copies of the gene will have dissimilar alleles and heterozygosity (i.e., the percentage of heterozygous genotypes in a population). So far, only a small part of the total genetic diversity, including date palm, has been characterized, evaluated, and used for crop breeding and improvement purposes (Dhanapal 2012 ). Sexual expression in palms is spatially separated at fi ve discrete levels; these are within fl owers (in between fl oral organs), within fl ower clusters (in between fl owers), within infl orescences (in between partial infl orescences), within palms (in between infl orescences), and in between palms.…”

“…Molecular markers are more precise and can accurately identify date palm cultivars and quantify their genetic diversity and phylogenic relationships. Molecular markers (i.e., DNA based) helped in the verifi cation of accession identity and genetic contamination and also have been used to identify ecogeographic landraces within the domesticated or wild gene pool of several crop species (Dhanapal 2012 ;Gao et al 2012 ). Several of these markers have been extensively used to study the genetic variation of date palm cultivars.…”

“…2.6 ). Population genetic differentiation is usually shaped by several factors, including species life history and environmental attributes affecting dispersal of either propagules (e.g., offshoots) or adult trees (Dhanapal 2012 ;Elshibli and Korpelainen 2009a , b ), where environmental and ecological distances proved to be better predictors of genetic differentiation between populations than simple geographic distances. The relationships between population differentiation based on molecular markers and each of heterozygosity and fi xation index across three studies is illustrated in Fig.…”