Genetic diversity determined by agronomic traits and SSR markers in two South American orange‐fleshed sweetpotato breeding populations with potential for population hybrid breeding

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 among tropical maize inbred lines as revealed by SSR markers

Australian Journal of Crop Science ◽

10.21475/ajcs.20.14.12.1589.pdf ◽

2020 ◽

pp. 2010-2019

Author(s):

Maizura Abu Sin ◽

Ghizan Saleh ◽

Nur Ashikin Psyquay Abdullah ◽

Pedram Kashiani

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Similarity Index ◽

Inbred Lines ◽

Hybrid Breeding ◽

Heterotic Groups ◽

Breeding Programs ◽

Maize Inbred Lines

Genetic diversity and phenotypic superiority are important attributes of parental inbred lines for use in hybrid breeding programs. In this study, genetic diversity among 30 maize (Zea mays L.) inbred lines comprising of 28 introductions from the International Maize and Wheat Improvement Center (CIMMYT), one from Indonesia and a locally developed, were evaluated using 100 simple sequence repeat (SSR) markers, as early screening for potential parents of hybrid varieties. All markers were polymorphic, with a total of 550 unique alleles detected on the 100 loci from the 30 inbred lines. Allelic richness ranged from 2 to 13 per locus, with an average of 5.50 alleles (na). Number of effective alleles (ne) was 3.75 per locus, indicating their high effectiveness in revealing diversity among inbred lines. Average polymorphic information content (PIC) was 0.624, with values ranging from 0.178 to 0.874, indicating high informativeness of the markers. High gene diversity was observed on Chromosomes 8 and 4, with high number of effective alleles, indicating their potential usefulness for QTL analysis. The UPGMA dendrogram constructed identified four heterotic groups within a similarity index of 0.350, indicating that these markers were able to group the inbred lines. The three-dimensional PCoA plot also supports the dendrogram grouping, indicating that these two methods complement each other. Inbred lines in different heterotic groups have originated from different backgrounds and population sources. Information on genetic diversity among the maize inbred lines are useful in developing strategies exploiting heterosis in breeding programs

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Genetic diversity and population structure of six South African Acacia mearnsii breeding populations based on SSR markers

Journal of Plant Research ◽

10.1007/s10265-021-01331-2 ◽

2021 ◽

Author(s):

Michael W. Bairu ◽

Assefa B. Amelework ◽

Willem G. Coetzer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

South African ◽

Ssr Markers ◽

Acacia Mearnsii ◽

Breeding Populations

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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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Changes of genetic diversity of maize inbred lines over four decades of hybrid breeding in the Bc institute revealed by SSR markers

Genetika ◽

10.2298/gensr1501233b ◽

2015 ◽

Vol 47 (1) ◽

pp. 233-243

Author(s):

Ivica Buhinicek ◽

Mirko Jukic ◽

Hrvoje Sarcevic ◽

Jerko Gunjaca ◽

Zdravko Kozic ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Inbred Lines ◽

Hybrid Breeding ◽

Maize Breeding ◽

Hybrid Production ◽

The Past ◽

Maize Inbred Lines ◽

Heterotic Pattern ◽

Private Alleles

In this paper, changes of genetic diversity of the most important maize inbred lines used for hybrid production within the Bc Institute in the 1970s, 1980s, 1990s and 2000s were examined using the SSR markers. The average number of alleles per SSR locus was 3.14, 3.43, 3.07 and 3.25 for lines from 1970s, 1980s, 1990s and 2000s, whereas the number of private alleles for the same four decades was 8, 4, 0 and 6, respectively. Mean genetic distance among inbreds within decades steadily decreased over time from 0.64 in 1970s to 0.57 in 2000s, but the observed differences were not statistically significant. The clustering of the studied inbred lines indicates the exploitation of a known BSSS x LSC heterotic pattern within the Bc Institute maize breeding program. The overall results show that recycled inbred lines within these pools do not decline in genetic variation over the past 40 years.

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