Identification and Characterization of Chickpea Genotypes for Early Flowering and High Seed Germination through Molecular Markers

Abstract Chickpea is the fourth most important legume crop contributing 3.1% to the total legume production and rich source of proteins, minerals and vitamins. Genetic diversity of wild and elite cultivar is quintessential for variety improvement. Determination of genetic diversity is more reliable and accurate, therefore, commonly used. In the present study, we analyzed the genetic diversity, population structure, cross-species transferability and allelic richness in 50 chickpea collection using 23 ISSR markers. The observed parameters such as allele number varied from 3 to 16,and polymorphic information content (PIC) varied from 0.15 to 0.4988, respectively. Further, range of allele size varied from 150 to 1600 bp, which shows the significance of ISSR markers for chickpea germplasm characterization. On the basis of ISSR marker genotypic data, dendrogram was constructed which divides these 50 chickpea in group I and II showing the reliability of ISSR markers. Among 50 chickpea, the accession P 74-1 is in group I and rest are in group II. Further we made mini-core collection of 15 diverse chickpea and sub-grouped them. Dendrogram, PCA, Dissimilarity matrix and Bayesian model based genetic clustering of 50 chickpea germplasms revealed that P 74-1 and P 1883are very diverse chickpea accession. Further selected 15 diverse chickpea screened for early flowering and high seed germination. Among 15 diversechickpea germplasms P 1857-1 and P 3971 has early flowering and high seed germination compared to P 1883 and other germplasm. Characterization of these diverse chickpea for early flowering and high seed germinationwould help in reducing crop duration and enhancing seed qualities. Utilization of these ISSRs markers in diversity analysis and population structure characterization of 50 chickpea germplasm suggests their wider efficacy for molecular breeding ofearly flowering and high seed germination.

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Population structure and genetic diversity of chickpea germplasms

10.1101/2021.08.04.455107 ◽

2021 ◽

Author(s):

Deepanshu jayaswal ◽

garima Yadav ◽

Kuldip Jayaswall ◽

Abhishek Bhandawat ◽

Arvind Nath Singh ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Structure Characterization ◽

Diversity Analysis ◽

Dissimilarity Matrix ◽

Group I ◽

Elite Cultivar

In various leguminous crops, chickpea is the fourth most important legume contributing 3.1% to the total legume production. Grains of chickpea are rich source of proteins, minerals and vitamins which makes them suitable for both food and feed. For any crop to be improved, the knowledge of genetic diversity of wild and elite cultivar is very important. Therefore among various available marker systems, molecular markers are more reliable and accurate, therefore are very commonly used for genetic diversity analysis, phylogenetic studies and cultivar identification. Due to several advantages of Inter Simple Sequence Repeat (ISSR) markers in present study we analyzed the genetic diversity, structure, cross-species transferability and allelic richness in 50 chickpea collection using 23 ISSR markers. The observed parameters such as allele number varied from 3 to 16, and PIC varied from 0.15 to 0.4988 respectively. Further, range of allele size varied from 150 to 1600 bp which shows the significance of ISSR markers for chickpea germplasms characterization. On the basis of ISSR marker genotypic data dendrogram were constructed which divides these 50 chickpea in group I and II showing the reliability of ISSR markers. Among 50 chickpea, the accession P 74-1 is in group I and rest are in group II. Further we made mini-core collection of 15 diverse chickpea and subgrouped them. Dendrogram, PCA, Dissimilarity matrix and Bayesian model based genetic clustering of 50 chickpea germplasms revealed that P 74-1,P 1883, P 1260 very diverse chickpea accession. Characterization of these diverse chickpea would help in maintenance breeding, conservation and in future could be used to develop climate resilient elite cultivar of chickpea. Utilization of these novel ISSRs markers in diversity analysis and population structure characterization of 50 chickpea germplasm suggests their wider efficacy in superior scale for molecular breeding studies in chickpea.

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Analyses of genetic diversity and population structure of anchote (Coccinia abyssinica (Lam.) Cogn.) using newly developed EST-SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01132-5 ◽

2021 ◽

Author(s):

Bekele Serbessa Tolera ◽

Kifle Dagne Woldegebriel ◽

Abel Teshome Gari ◽

Mulatu Geleta Dida ◽

Kassahun Tesfaye Geletu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Citrullus Lanatus ◽

Wide Range ◽

Minor Crop ◽

Ssrs Markers ◽

Expressed Sequence

AbstractAnchote (Coccinia abyssinica (Lam.) Cogn.) is a perennial root crop belonging to Cucurbitaceae family. It is endemic to Ethiopia and distributed over wide range of agro-ecologies. For further improvement and efficient conservation of this crop, characterization of its genetic diversity and its pattern of distribution is a vitally important step. Expressed sequence tags-simple sequence repeats (EST-SSRs) markers were developed from publicly available watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] ESTs in the GenBank database. Among those novel markers, eight were polymorphic and subsequently used for genetic diversity and population structure analyses of 30 anchote accessions collected from western Ethiopia. A total of 24 alleles were obtained across the eight polymorphic loci and 30 accessions that revealed moderate level of genetic diversity in this minor crop. Among the eight loci, locus CA_06 was the most informative with six alleles and polymorphic information content (PIC) of 0.76. The accessions showed about threefold variation in terms of genetic diversity, with expected heterozygosity (He) ranging from 0.15 (accession An) to 0.44 (accession Dg). Other accessions with higher genetic diversity include Ar and Gu (He = 0.43 and 0.41, respectively). Analysis of molecular variance (AMOVA) revealed that the variation within accessions and among accessions accounted for 84.7% and 15.3% of the total variation, respectively. The study revealed low but significant population differentiation in this crop with no clear pattern of population structure. The EST-SSR markers developed in this study are the first of their kind for anchote and can be used for characterization of its wider genetic resources for conservation and breeding purposes.

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Genetic Diversity Analysis and Population Structure in Apricot (Prunus Armeniaca L.) Grown Under North-Western Himalayas Using ISSR Markers

Saudi Journal of Biological Sciences ◽

10.1016/j.sjbs.2021.06.051 ◽

2021 ◽

Author(s):

Zahid Nabi Sheikh ◽

Vikas Sharma ◽

Rafiq Ahmad Shah ◽

Neha Sharma ◽

Baby Summuna ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Issr Markers ◽

Prunus Armeniaca ◽

Diversity Analysis ◽

Western Himalayas ◽

Genetic Diversity Analysis ◽

Prunus Armeniaca L ◽

North Western

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Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00168-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Workia Ahmed ◽

Tileye Feyissa ◽

Kassahun Tesfaye ◽

Sumaira Farrakh

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Information Content ◽

Date Palm ◽

Polymorphic Information Content ◽

Phoenix Dactylifera ◽

Mean Value ◽

Date Palms ◽

Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

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Genetic diversity and population structure of the mangrove lime (Merope angulata) in India revealed by AFLP and ISSR markers

Aquatic Botany ◽

10.1016/j.aquabot.2014.09.004 ◽

2015 ◽

Vol 120 ◽

pp. 260-267 ◽

Cited By ~ 12

Author(s):

Satya Narayan Jena ◽

Sushma Verma ◽

Kuttan Narayanan Nair ◽

Awadhesh Kumar Srivastava ◽

Sujata Misra ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Issr Markers

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Population structure of Chinese southwest wheat germplasms resistant to stripe rust and powdery mildew using the DArT-seq technique

Ciência Rural ◽

10.1590/0103-8478cr20160066 ◽

2018 ◽

Vol 48 (4) ◽

Cited By ~ 3

Author(s):

Tianqing Chen ◽

Piyada Alisha Tantasawat ◽

Wei Wang ◽

Xu Gao ◽

Liyi Zhang

Keyword(s):

Population Structure ◽

Disease Resistance ◽

Polymorphic Information Content ◽

Wheat Breeding ◽

Wheat Varieties ◽

Group I ◽

Population Structure Analysis ◽

Specific Allele ◽

The Mean ◽

Different Origins

ABSTRACT: Understanding genetic variability in existing wheat accessions is critical for collection, conservation and use of wheat germplasms. In this study, 138 Chinese southwest wheat accessions were investigated by genotyping using two resistance gene makers (Pm21 and Yr26) and DArT-seq technique. Finally, about 50% cultivars (lines) amplified the specific allele for the Yr26 gene (Gwm11) and 40.6% for the Pm21 gene (SCAR1265). By DArT-seq analysis, 30,485 markers (6486 SNPs and 23999 DArTs) were obtained with mean polymorphic information content (PIC) value 0.33 and 0.28 for DArT and SNP marker, respectively. The mean Dice genetic similarity coefficient (GS) was 0.72. Two consistent groups of wheat varieties were identified using principal coordinate analysis (PCoA) at the level of both the chromosome 6AS and the whole-genome, respectively. Group I was composed of non-6VS/6AL translocation lines of different origins, while Group II was composed of 6VS/6AL translocation (T6VS/6AL) lines, most of which carried the Yr26 and Pm21 genes and originated from Guizhou. Besides, a model-based population structure analysis revealed extensive admixture and further divided these wheat accessions into six subgroups (SG1, SG2, SG3, SG4, SG5 and SG6), based on their origin, pedigree or disease resistance. This information is useful for wheat breeding in southwestern China and association mapping for disease resistance using these wheat germplasms in future.

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ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

10.21203/rs.3.rs-666059/v1 ◽

2021 ◽

Author(s):

Lalit Arya ◽

Ramya Kossery Narayanan ◽

Anjali Kak ◽

Chitra Devi Pandey ◽

Manjusha Verma ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Morinda Citrifolia ◽

Species Differentiation ◽

Information Index ◽

Upgma Cluster Analysis ◽

Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

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