Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)
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 (<i>Oryza sativa</i>...
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MDPI AG
2023-07-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/13/7/1906 |
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| author | Paul Kitenge Kimwemwe Chance Bahati Bukomarhe Edward George Mamati Stephen Mwangi Githiri René Mushizi Civava Jacob Mignouna Wilson Kimani Mamadou Fofana |
| author_facet | Paul Kitenge Kimwemwe Chance Bahati Bukomarhe Edward George Mamati Stephen Mwangi Githiri René Mushizi Civava Jacob Mignouna Wilson Kimani Mamadou Fofana |
| author_sort | Paul Kitenge Kimwemwe |
| collection | DOAJ |
| description | 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 (<i>Oryza sativa</i> 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 (F<sub>st</sub> = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (H<sub>o</sub> = 0.08) was lower than expected heterozygosity (H<sub>e</sub> = 0.14) because of the high inbreeding (F<sub>is</sub> = 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. |
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| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-11T01:23:47Z |
| publishDate | 2023-07-01 |
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| series | Agronomy |
| spelling | doaj.art-ab8eaf623d9d400b9cd2972c74e8f7c12023-11-18T17:58:01ZengMDPI AGAgronomy2073-43952023-07-01137190610.3390/agronomy13071906Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)Paul Kitenge Kimwemwe0Chance Bahati Bukomarhe1Edward George Mamati2Stephen Mwangi Githiri3René Mushizi Civava4Jacob Mignouna5Wilson Kimani6Mamadou Fofana7Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, KenyaDepartment of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, KenyaDepartment of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, KenyaDepartment of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, KenyaInstitut National pour l’Etude et la Recherche Agronomiques (INERA), Kinshasa P.O. Box 2037, Democratic Republic of the CongoOlusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the CongoInternational Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, KenyaOlusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the CongoUnderstanding 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 (<i>Oryza sativa</i> 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 (F<sub>st</sub> = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (H<sub>o</sub> = 0.08) was lower than expected heterozygosity (H<sub>e</sub> = 0.14) because of the high inbreeding (F<sub>is</sub> = 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.https://www.mdpi.com/2073-4395/13/7/1906population structuregenetic diversityrice germplasmDArTseqsingle nucleotide polymorphism |
| spellingShingle | Paul Kitenge Kimwemwe Chance Bahati Bukomarhe Edward George Mamati Stephen Mwangi Githiri René Mushizi Civava Jacob Mignouna Wilson Kimani Mamadou Fofana Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP) Agronomy population structure genetic diversity rice germplasm DArTseq single nucleotide polymorphism |
| title | Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP) |
| title_full | Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP) |
| title_fullStr | Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP) |
| title_full_unstemmed | Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP) |
| title_short | Population Structure and Genetic Diversity of Rice (<i>Oryza sativa</i> L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP) |
| title_sort | population structure and genetic diversity of rice i oryza sativa i l germplasm from the democratic republic of congo drc using dartseq derived single nucleotide polymorphism snp |
| topic | population structure genetic diversity rice germplasm DArTseq single nucleotide polymorphism |
| url | https://www.mdpi.com/2073-4395/13/7/1906 |
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