Genetic diversity of cucumber genotypes revealed by SSR markers and agronomic traits

Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.

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Genetic Diversity of Shanlan Upland Rice (Oryza sativa L.) and Association Analysis of SSR Markers Linked to Agronomic Traits

BioMed Research International ◽

10.1155/2021/7588652 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Guofeng Yang ◽

Yong Yang ◽

Yali Guan ◽

Zhixia Xu ◽

Junyu Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Height ◽

Ssr Markers ◽

Agronomic Traits ◽

Upland Rice ◽

Diversity Index ◽

Oryza Sativa L ◽

Grain Number ◽

Rice Germplasm ◽

Panicle Number

Shanlan upland rice, a kind of unique rice germplasm in Hainan Island, was used to evaluate genetic diversity and association between SSR markers and agronomic traits. A total of 239 alleles were detected in 57 Hainan upland rice varieties using 35 SSR markers, and the number of alleles per locus was 2-19. The observed heterozygosity was 0.0655-0.3115. The Shannon diversity index was 0.1352-0.4827. The genetic similarity coefficient was 0.6736-0.9707, and 46 varieties were clustered into one group, indicating that the genetic base of the Shanlan upland rice germplasm was narrow. A total of 25 SSR markers significantly related to plant height, effective panicle number per plant, panicle length, total grain number, filled grain number, seed rating rate, and 1000-grain weight were obtained ( P < 0.01 ), with the percentage of the total variations explained ranging from 0.12% to 42.62%. RM208 explained 42.62% of the total variations in plant height of Shanlan upland rice. RM493 was significantly associated with 6 agronomic traits. We can speculate that RM208 may flank QTLs responsible for plant height and RM493 may flank QTLs playing a fundamental role in the intertwined regulatory network of agronomic traits of Shanlan upland rice.

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Assessment of genetic diversity in cultivated radishes ( Raphanus sativus ) by agronomic traits and SSR markers

Scientia Horticulturae ◽

10.1016/j.scienta.2017.05.025 ◽

2017 ◽

Vol 223 ◽

pp. 19-30 ◽

Cited By ~ 3

Author(s):

O New Lee ◽

Han Yong Park

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Raphanus Sativus ◽

Agronomic Traits

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Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.)

Plants ◽

10.3390/plants10102112 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2112

Author(s):

Xiaohan Wang ◽

Myung Chul Lee ◽

Yu-Mi Choi ◽

Seong-Hoon Kim ◽

Seahee Han ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Association Analysis ◽

Agronomic Traits ◽

Fixation Index ◽

Total Phenolic ◽

Panicum Miliaceum ◽

Proso Millet ◽

Population Structure Analysis

Proso millet (Panicum miliaceum L.) or broomcorn millet is among the most important food crops to be domesticated by humans; it is widely distributed in America, Europe, and Asia. In this study, we genotyped 578 accessions of P. miliaceum using 37 single-sequence repeat (SSR) markers, to study the genetic diversity and population structure of each accession. We also investigated total phenolic content (TPC) and superoxide dismutase (SOD) activity and performed association analysis using SSR markers. The results showed that genetic diversity and genetic distance were related to geographic location and the fixation index (Fst). Population structure analysis divided the population into three subpopulations. Based on 3 subpopulations, the population is divided into six clusters in consideration of geographical distribution characteristics and agronomic traits. Based on the genetic diversity, population structure, pairwise Fst, and gene flow analyses, we described the topological structure of the six proso millet subpopulations, and the geographic distribution and migration of each cluster. Comparison of the published cluster (cluster 1) with unique germplasms in Japan and South Korea suggested Turkey as a possible secondary center of origin and domestication (cluster 3) for the cluster. We also discovered a cluster domesticated in Nepal (cluster 6) that is adapted to high-latitude and high-altitude cultivation conditions. Differences in phenotypic characteristics, such as TPC, were observed between the clusters. The association analysis showed that TPC was associated with SSR-31, which explained 7.1% of the total variance, respectively. The development of markers associated with TPC and SOD will provide breeders with new tools to improve the quality of proso millet through marker-assisted selection.

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Analysis of Population Structure and Genetic Diversity in Rice Germplasm Using SSR Markers: An Initiative Towards Association Mapping of Agronomic Traits in Oryza Sativa

Rice ◽

10.1186/s12284-015-0062-5 ◽

2015 ◽

Vol 8 (1) ◽

Cited By ~ 61

Author(s):

Vishnu Varthini Nachimuthu ◽

Raveendran Muthurajan ◽

Sudhakar Duraialaguraja ◽

Rajeswari Sivakami ◽

Balaji Aravindhan Pandian ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Oryza Sativa ◽

Association Mapping ◽

Ssr Markers ◽

Agronomic Traits ◽

Rice Germplasm

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GENETIC DIVERSITY ASSOCIATED WITH AGRONOMIC TRAITS AND BIOTIC STRESSES USING SSR MARKERS IN SOME EGYPTIAN RICE GENOTYPES

Journal of Plant Production ◽

10.21608/jpp.2011.85469 ◽

2011 ◽

Vol 2 (1) ◽

pp. 109-126

Author(s):

Y. El-Refaee ◽

S. Sedeek ◽

R. El-Shafey ◽

B. Zayed

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Agronomic Traits ◽

Biotic Stresses ◽

Rice Genotypes

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Assessment of Genetic Diversity Among Intra- and Interspecific Lowland Rice using Morpho-agronomic Traits and SSR Markers

10.21203/rs.3.rs-816797/v1 ◽

2021 ◽

Author(s):

Ayoni Ogunbayo ◽

Moussa Sié ◽

Glenn B. Gregorio ◽

David Kolawole Ojo ◽

Kayode Abiola Sanni ◽

...

Keyword(s):

Genetic Diversity ◽

Total Variation ◽

Ssr Markers ◽

Agronomic Traits ◽

Structured Populations ◽

Lowland Rice ◽

Oryza Glaberrima ◽

Environment Interaction ◽

Rice Genotypes ◽

Benin Republic

Abstract Rice is staple food in many countries of Africa and a major part of the diet in many others. However, Africa’s demand for rice exceeds production with the deficit of 40% being imported. One way to improve Africa’s rice production is through breeding high yielding varieties suitable for the different environment conditions. This study was conducted to assess the genetic variability and stability performance of 48 lowland rice genotypes including 37 interspecific (Oryza glaberrima × Oryza sativa ssp. indica) and 11 intraspecific (O. sativa ssp. indica × O. sativa ssp. indica) in 12 environments in Nigeria, Benin Republic and Togo using Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype+ Genotype x Environment (GGE) biplot models. The combined analysis of variance revealed significant differences (P<0.01) among the genotypes, environments, and genotypes x environment interaction. Both the AMMI and GGE models identified NERICA-L8 and NERICA-LI2 as the best genotypes for cultivation across environments. Ouedeme environments in Benin Republic were the most stable and ideal for rice cultivation, while Ibadan sites were the most unstable. TOG 5681 had the least yield and was the most unstable across seasons. Genetic diversity was analyzed using 22 important morpho-agronomic traits and 50 simple sequence repeat (SSR) markers and the results were subjected to principal components analysis (PCA). The results revealed that the first eight PC axes (PC1–8) accounted for 75.13% of the total variation, while PC1–4 accounted for 50.39% of the total variation among rice genotypes. However, 10 of the 50 SSR markers were polymorphic and generated 49 alleles (average = 4.9 alleles per locus), suggesting moderate to substantial genetic diversity among the rice genotypes. The polymorphic information content (PIC) ranged from 0.24 to 0.65, with an average PIC value of 0.45. Two structured populations were observed which clustered into five heterotic groups and an outgroup, respectively. This suggests that heterosis could be exploited in the next hybridization program by crossing one of the genotypes in any SSR marker-defined cluster, with the rice accession TOG 5681 in cluster I. The results of this study suggest that morpho-agronomic traits should be used to compliment SSR data in rice diversity studies, especially if a few polymorphic SSR markers are to be used.

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