Morphology and SSR Markers-Based Genetic Diversity Analysis of Sesame (Sesamum indicum L.) Cultivars Released in China

Abstract

Sesame is a highly valuable crop with significant global importance due to its nutritional and economic value. To better understand the genetic diversity of sesame genotypes at both molecular and morphological levels, a comprehensive study was conducted using 25 pairs of simple sequence repeat (SSR) primers and 56 biological traits in a collection of 183 sesame accessions, which comprised 101 Chinese cultivars, 62 landraces, and 20 exotic accessions. The analysis revealed a total of 166 SSR polymorphic bands, with an average of 6.64 bands per marker. The values of Shannon’s information index ranged from 0.2732 to 0.6497, indicating a moderate level of genetic diversity. The polymorphic information index ranged from 0.0859 to 0.6357, further supporting the presence of genetic variation. The average frequency of heterozygous genotypes was calculated as 0.34, suggesting a relatively narrow genetic diversity. The application of the unweighted pair group method with arithmetic averaging (UPGMA) clustering and principal component analysis allowed for the categorization of the 183 sesame accessions into three distinct groups. Furthermore, the genetic diversity coefficient of sesame germplasm is generally constrained, with no significant difference observed between the genetic diversity coefficient of Chinese cultivars and that of foreign resources. The results provide valuable data for various applications, including the breeding and promotion of new sesame cultivars in China, the protection of new variety rights, the inquiry and identification of DNA genetic information of cultivars, as well as the development and utilization of sesame germplasm resources both domestically and internationally.

Genetic Diversity and Population Structure of a Large USDA Sesame Collection

“…Approximately 1.3% of the genotyped SNPs had a He ≤ 0.100, while 58% had a He ≥ 0.300 (Figure 3A). These results were slightly lower than the reported He values in sesame [5,38] using a lower number of SSR markers. Perhaps these discrepancies in the He values can be explained by the effects of the population size and diversity as well as the molecular marker types and allele numbers per locus.…”

“…It is a fundamental step in studying the genetic relationships among and within crop populations to improve their productivity and responses to environments. To reach this goal, phenotypic and genetic diversity studies were conducted to explore the variations in sesame populations [4][5][6]10,[12][13][14][15][16][17][18][19][20][21][22][23]25,[35][36][37][38]. In this study, we employed NGS-GBS technology to gain a deep understanding of the USDA sesame collection and study the genetic relationships among its accessions.…”

“…The number of sesame subpopulations identified in previous studies varied based on the population size, the origin of the genotypes, and the number and type of molecular markers used. For example, previous research has grouped sesame populations into two [7,10,37,38], three [5,12,19,65], or four subpopulations [4,25]. The current results indicated that sesame subpopulation 1 included 256 accessions that were mainly collected from Asia (133 accessions), where 78 accessions were collected from eastern Asia, while subpopulation 2 consisted of 245 accessions, with 121 being collected from Asia (108 from the Indian subcontinent) and 93 being collected from Africa (65 from Sudan) (Supplementary Table S1).…”

“…As such, it has been made possible to expedite the Plants 2024, 13, 1765 2 of 16 discovering of genes and alleles controlling these traits via genome-wide association studies (GWAS), genetic mapping, and omics approaches such transcriptomics, metabolomics, and lipidomics, and the selection of parental accessions for use in conventional plant breeding techniques. As one of the important oil crops, sesame's germplasm and accessions were characterized both phenotypically [4][5][6][7][8][9] and genetically [10][11][12], indicating the possibility of improving sesame for high productivity and biotic and abiotic stress tolerance [5,13,14]. Sesame's genetic diversity was assayed using different types of biochemical [15] and molecular markers, among which were random amplified polymorphic DNA (RAPD) [16][17][18], simple sequence repeats (SSR) [4,5,19,20], inter-simple sequence repeats (ISSR) [11,21], amplified fragment length polymorphism (AFLP) [7,22], and sequence-related amplified polymorphism (SRAP) [23].…”

“…As one of the important oil crops, sesame's germplasm and accessions were characterized both phenotypically [4][5][6][7][8][9] and genetically [10][11][12], indicating the possibility of improving sesame for high productivity and biotic and abiotic stress tolerance [5,13,14]. Sesame's genetic diversity was assayed using different types of biochemical [15] and molecular markers, among which were random amplified polymorphic DNA (RAPD) [16][17][18], simple sequence repeats (SSR) [4,5,19,20], inter-simple sequence repeats (ISSR) [11,21], amplified fragment length polymorphism (AFLP) [7,22], and sequence-related amplified polymorphism (SRAP) [23]. Utilizing next-generation sequencing (NGS) technologies reduced the genotyping time and effort required to genotype thousands of genotypes and, thus, reduce the cost, which has made single-nucleotide polymorphism (SNP) markers the most common marker type for genome-wide studies [24], where SNPs are biallelic markers that are uniformly distributed throughout the genomes.…”