Comparison of Genetic Diversity among Amaranth Accessions from South and Southeast Asia using SSR Markers

Abstract

: This study was conducted to assess the genetic diversity and population structure of 70 amaranth accessions collected from South and Southeast Asia using 14 simple sequence repeat (SSR) markers. In total, 67 alleles were detected, with an average of 4.79 per locus. Rare alleles comprised a large portion (46.3%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. The mean major allele frequency (MAF), genetic diversity (GD) and polymorphic information content (PIC) of the 14 SSR loci were 0.77, 0.36, and 0.34, respectively. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbor-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. All 70 accessions showed a clear relationship to each cluster without any admixtures. We observed a relatively low extent of genetic exchange within or among amaranth species from South and Southeast Asia. The genetic diversity results could be used to identify amaranth germplasms and so facilitate their use for crop improvement.

Genetic diversity of leafy amaranth (<i>Amaranthus tricolor</i> L.) resources in Vietnam

“…Subgroup 1 included mostly accessions from East Asia and Vietnam, and contained 90.7% of all East Asian accessions; subgroup 2 included mostly accessions from Vietnam and subgroup 3 from South Asia; and subgroup 4 included 60% of accessions from America ( Table 4). The results suggest association of the four subgroups with geographical areas and partly agree with the result of Wang and Park (2013), who claimed that the extent of genetic exchange within or among amaranth species from South and Southeast Asia is relatively low. On the other hand, Suresh et al (2014) used 11 SSR markers for STRUCTURE analysis of 348 amaranth accessions from 33 species and found no significant correlation between geographic distance and genetic diversity.…”

“…The 21 markers amplified a total of 153 alleles in 294 accessions with an average of 7.29 alleles per locus, Ho of 0.14, He of 0.38, and PIC of 0.35. The average allele richness in our study was larger than in Mallory et al (2008) and Wang and Park (2013) Vietnamese collection 119 13 5 12 13 10 9 19 9 29 Northeast 25 3 5 2 2 2 4 1 6 Northwest 25 4 1 1 5 3 2 1 1 7 Red River Delta 9 4 1 1 1 2 North Central Coast 18 1 3 1 4 3 6 South Central Coast 13 3 2 7 1 Central Highlands 12 1 3 1 2 1 1 3 Southeast 5 1 2 2 Southwest 12 1 1 2 2 1 1 1 3 a Subgroup. b Membership probabilities Q > 0.75.…”

“…However, the development of SSRs is labor-intensive, economically costly, and time-consuming (Taheri et al 2018). Studies on the genetic diversity of amaranths were based only on 11-14 SSR markers (Khaing et al 2013, Kietlinski et al 2014, Lee et al 2008, Mallory et al 2008, Singh et al 2013, Suresh et al 2014, Wang and Park 2013. These markers were developed by Mallory et al (2008) and Lee et al (2008) on the basis of genomic DNA of A. hypochondriacus L. The advent of the high throughput sequencing technology along with bioinformatics tools has facilitated fast discovery of thousands of potentially amplifiable microsatellite regions at low cost, even for species with limited genomic information (Guichoux et al 2011, Silva et al 2013, Taheri et al 2018, Zalapa et al 2012.…”

Genetic Diversity of Black Amaranth (Amaranthus quitensis Kunth) Landraces of Ecuadorian Highlands: Association Genotypes—Color Morphotypes

“…Microsatellite markers have been developed for the genus Amaranthus by Mallory et al [47] and Lee et al [48] on the basis of the genomic DNA of A. hypochondriacus, and they have successfully amplified in other amaranth species. Several studies to assess the genetic and structural diversity in different amaranth species have used many of these SSR markers [5,6,10,42,49,50]. Recently, Nguyen et al [28] have also developed new SSR markers from the genome sequence of the A. tricolor cultivar 'Biam' to evaluate the genetic diversity of Vietnamese accessions of this species.…”

Genetic diversity analysis and molecular characterization of grain amaranth genotypes using inter simple sequence repeat (ISSR) markers

“…Molecular phylogenetic studies would enable plant breeders to discriminate among genotypes by estimating the extent of variation within and between species which provides a base for appropriate breeding approaches. Well established molecular markerbased techniques such as random amplified polymorphic DNAs (RAPDs) (Faseela and Joseph 2007;Ray and Roy 2008;Popa et al 2010;Snezana et al 2012;Anjali et al 2013), restriction fragment length polymorphisms (RFLPs) (Park et al 2014), simple sequence repeats (SSRs) (Mallory et al 2008;Suresh et al 2014;Wang and Park 2013), amplified fragment length polymorphisms (AFLPs) (Chandi et al 2013), inter-simple sequence repeats (ISSRs) (Nolan et al 2010;Singh et al 2013;Raut et al 2014;Stefunova et al 2014), and single nucleotide polymorphisms (SNPs) (Jimenez et al 2013) have been utilized in genetic diversity studies in Amaranthus species. These molecular markers vary in their level of polymorphism, genomic abundance, reproducibility, locus specificity, dominance or codominance, technical desires, and economic investment (Zietkiewicz et al 1994;Omondi et al 2016).…”