Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers

Mudaki, Phoebe; Wamalwa, Lydia N.; Muui, Catherine W.; Nzuve, Felister M.; Muasya, Reuben M.; Nguluu, Simon N.; Kimani, Wilson

doi:10.1007/s00239-023-10108-1

Cited by 5 publications

(2 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…DArTseq further reduces genome representation and provides abundant markers [26], thus improving the rate of genotype calling and the ability to sequence more samples at a lower cost. DArTseq produces both dominant (SilicoDArT) and co-dominant (SNP) markers that have successfully been applied for genetic diversity and population structure analysis in several crops such as cassava [27], taro [28], rice [29], rye [30], sorghum [31], and wheat [19]. The use of DArTseq markers enables a comprehensive analysis of genetic diversity, complete genome profiling, and high-density mapping of complex traits, all of which are crucial for marker-based breeding [24].…”

Section: Introductionmentioning

confidence: 99%

Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)

Kimwemwe,

Bukomarhe,

Mamati

et al. 2023

Agronomy

Self Cite

View full text Add to dashboard Cite

Understanding the genetic diversity and population structure of rice is crucial for breeding programs, conservation efforts, and the development of sustainable agricultural practices. This study aimed to assess the genetic diversity and population structure of 94 rice (Oryza sativa L.) genotypes from the Democratic Republic of Congo using a set of 8389 high-quality DArTseq-based single nucleotide polymorphism (SNP) markers. The average polymorphic information content (PIC) of the markers was 0.25. About 42.4% of the SNPs had a PIC value between 0.25 and 0.5, which were moderately informative. The ADMIXTURE program was used for structure analysis, which revealed five sub-populations (K = 5), with admixtures. In principal component analysis (PCA), the first three principal components accounted for 36.3% of the total variation. Analysis of molecular variance revealed significant variation between sub-populations (36.09%) and within genotypes (34.04%). The low overall number of migrants (Nm = 0.23) and high fixation index (Fst = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (Ho = 0.08) was lower than expected heterozygosity (He = 0.14) because of the high inbreeding (Fis = 0.52) nature of rice. A high average Euclidean genetic distance (0.87) revealed the existence of genetic diversity among the 94 genotypes. The significant genetic diversity among the evaluated rice genotypes can be further explored to obtain potentially desirable genes for rice improvement.

show abstract

Section: Introductionmentioning

confidence: 99%

Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)

Kimwemwe,

Bukomarhe,

Mamati

et al. 2023

Agronomy

Self Cite

View full text Add to dashboard Cite

show abstract

“…The alignment efficiency between the results of this study and the reference genome is from 70.26% to 97.27%, which reveals that there are differences in the whole-genome sequence of the materials studied. The average ratio of Ts/Tv is 1.54; similar rates exist in other plants, like sweet cherry and sorghum [ 51 , 52 ]. Furthermore, some reports suggest that high Ts/Tv ratios indicate low levels of genetic differentiation in genomic comparisons [ 53 ].…”

Section: Discussionmentioning

confidence: 63%

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Zhou,

Liu,

et al. 2024

Plants

View full text Add to dashboard Cite

Rubus chingii Hu is the only species that is used for both edible and medicinal purposes among the 194 species of the genus Rubus in China. It is well known for its sweet and sour fresh fruits that are rich in vitamins and for its dried immature fruits that are used to treat kidney-related ailments. This study aims to evaluate genetic diversity and population structure and build a core germplasm repository of 132 R. chingii accessions from the provinces of Jiangxi and Fujian, using Hyper-seq-derived single-nucleotide polymorphism (SNP) markers. This is the first genetic study of R. chingii based on SNP molecular markers, and a total of 1,303,850 SNPs and 433,159 insertions/deletions (InDels) were identified. Low values for observed heterozygosity, nucleotide diversity (Pi) and fixation indexes (Fis) indicated low genetic diversity within populations, and an analysis of molecular variance (AMOVA) showed that 37.4% and 62.6% of the variations were found between populations and within samples, respectively. Four main clusters were identified by means of neighbor-joining (NJ) trees, the ADMIXTURE program and principal component analysis (PCA). Based on the genetic diversity, we finally constructed 38 representative core collections, representing 50% of the total core germplasm samples and 95.3% of the genotypes. In summary, the results of our study can provide valuable information on the genetic structure of R. chingii germplasm resources, which is helpful for further explorations of potential high-quality genes and for formulating future breeding and conservation strategies.

show abstract

Genetic diversity of a Silybum marianum (L.) Gaertn. germplasm collection revealed by DNA Diversity Array Technology (DArTseq)

Puglisi,

Pasquariello,

Martinelli

et al. 2024

PLoS ONE

View full text Add to dashboard Cite

Silybum marianum (L.) Gaertn. is a multipurpose crop native to the Mediterranean and middle east regions and mainly known for the hepatoprotective properties of fruit-derived silymarin. Despite growing interest in milk thistle as a versatile crop with medicinal value, its potential in agroindustry is hindered by incomplete domestication and limited genomic knowledge, impeding the development of competitive breeding programs. The present study aimed to evaluate genetic diversity in a panel of S. marianum accessions (n = 31), previously characterized for morphological and phytochemical traits, using 5,178 polymorphic DArTseq SNP markers. The genetic structure investigated using both parametric and non-parametric approaches (e.g. PCA, AWclust, Admixture), revealed three distinctive groups reflecting geographical origins. Indeed, Pop1 grouped accessions from Central Europe and UK, Pop3 consisted mainly of accessions of Italian origin, and Pop2 included accessions from different geographical areas. Interestingly, Italian genotypes showed a divergent phenotypic distribution, particularly in fruit oleic and linoleic acid content, compared to the other two groups. Genetic differentiation among the three groups, investigated by computing pairwise fixation index (FST), confirmed a greater differentiation of Pop3 compared to other subpopulations, also based on other diversity indices (e.g. private alleles, heterozygosity). Finally, 22 markers were declared as putatively under natural selection, of which seven significantly affected some important phenotypic traits such as oleic, arachidonic, behenic and linoleic acid content. These findings suggest that these markers, and overall, the seven SNP markers identified within Pop3, could be exploited in specific breeding programs, potentially aimed at diversifying the use of milk thistle. Indeed, incorporating genetic material from Pop3 haplotypes carrying the selected loci into milk thistle breeding populations might be the basis for developing milk thistle lines with higher levels of oleic, arachidonic, and behenic acids, and lower levels of linoleic acid, paving new avenues for enhancing the nutritional and agronomic characteristics of milk thistle.

show abstract

Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers

Cited by 5 publications

References 57 publications

Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)

Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)

Genetic Diversity Analysis and Core Germplasm Construction of Rubus chingii Hu

Genetic diversity of a Silybum marianum (L.) Gaertn. germplasm collection revealed by DNA Diversity Array Technology (DArTseq)

Contact Info

Product

Resources

About