Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

Abstract

BackgroundSesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC).ResultsResults from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven.ConclusionsThis study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR% suggested that the MC provides a good representation of the genetic diversity of the original CC. The MC was more genetically diverse with higher diversity indices and a higher PIC value than the CC. A MC may aid in reasonably and efficiently selecting materials for sesame breeding and for genotypic biological studies, and may also be used as a population for association mapping in sesame.

Deep resequencing reveals allelic variation in Sesamum indicum

“…To overcome environmental stresses and improve yields, abundant germplasm along with genetic information are required for plant-breeding programs [1], and characterization of genome-wide patterns of allele variation and linkage disequilibrium ensure the detection of reliable phenotype–genotype associations and signatures of molecular selection [2]. India, China and Korea are the leading countries for sesame germplasm collection, preservation and research [3]. In China, ~6,000 strains of sesame have been deposited in the National Gene Bank of China (Wuhan, medium-term Genebank; Beijing, long-term Genebank).…”

SesameFG: an integrated database for the functional genomics of sesame

“…Although more than 35,000 accessions of sesame have been conserved in the major crop germplasm genebanks of the world and their important agronomic traits have been investigated 30–32 , little phenotypic information of the sesame germplasm is available online. Therefore, it is quite difficult for sesame researchers to find a superior germplasm used for functional genomics research from the existing gene banks.…”

“…To identify valuable germplasm with superior alleles, the precise phenotypic information of the germplasm is required. Many germplasm resources have been collected in several sesame germplasm banks 30–32 , and the important agronomic traits of these germplasms have been observed. However, little phenotypic information of these germplasms is available online.…”

Establishing an Efficient Way to Utilize the Drought Resistance Germplasm Population in Wheat

“…A valid core collection provides a high-efficient way to assess genetic diversity or to find beneficial genes [21–24]. Most core collection researches focused on finding efficient ways in sub-core collection selection [25–27].…”