Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers

Abstract Background The genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers. Methods and results A total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean. Conclusion In the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar’s pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

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Analysis of Genetic Diversity in the Brassica napus L. Gene Pool Using SSR Markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-004-5541-2 ◽

2005 ◽

Vol 53 (4) ◽

pp. 793-802 ◽

Cited By ~ 104

Author(s):

M. Hasan ◽

F. Seyis ◽

A. G. Badani ◽

J. Pons-Kühnemann ◽

W. Friedt ◽

...

Keyword(s):

Genetic Diversity ◽

Brassica Napus ◽

Ssr Markers ◽

Gene Pool ◽

Brassica Napus L

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The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species

Plant Genetic Resources ◽

10.1079/pgr200454 ◽

2005 ◽

Vol 3 (1) ◽

pp. 19-28 ◽

Cited By ~ 12

Author(s):

Sally L. Dillon ◽

Peter K. Lawrence ◽

Robert J. Henry

Keyword(s):

Genetic Diversity ◽

Sorghum Bicolor ◽

Ssr Markers ◽

Diversity Indices ◽

Basic Knowledge ◽

Apparent Lack ◽

Breeding Programmes ◽

Diversity Studies ◽

Potential Use ◽

Simple Sequence

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

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Study of the gene pool of the winter rye Secale cereale L. of the Republic of Belarus using microsatellite markers

Proceedings of the National Academy of Sciences of Belarus Biological Series ◽

10.29235/1029-8940-2021-66-2-215-222 ◽

2021 ◽

Vol 66 (2) ◽

pp. 215-222

Author(s):

V. S. Mandrusova ◽

I. S. Gordej ◽

O. M. Lyusikov ◽

V. E. Shimko ◽

I. A. Gordej

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Ssr Markers ◽

Gene Pool ◽

Winter Rye ◽

Interpopulation Variability ◽

Content Index ◽

Secale Cereale L ◽

New Varieties ◽

The Republic

In this work, the genetic diversity of the modern gene pool of the winter rye (S. cereal L.) of the Republic of Belarus from 20 actual breeding samples was investigated using 15 microsatellite (SSR) markers to develop divergent crossing combinations in breeding for heterosis. It was shown that the formed set of SSR markers is highly effective – the informational content index (PIC) varied from 0.50 to 0.83 and averaged 0.72. The most effective microsatellite markers (SCM28, SCM43, SCM101 and SCM102) were identified and can be successfully used to study the genetic diversity of rye. It has been established that the modern gene pool of the winter rye of the Republic of Belarus is generally characterized by fairly wide genetic diversity (interpopulation variability) – all collection samples are characterized by a unique allelic composition of the studied microsatellite loci. Based on investigation results, a hierarchical clustering dendrogram was constructed, which made it possible to determine the most genetically divergent combinations of crosses. The information obtained can be used for the development of an effective scheme allowing to develop new varieties and hybrids in the practical breeding of rye for heterosis.

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The results of divergence of early-maturing maize source material in heterosis breeding

Plant varieties studying and protection ◽

10.21498/2518-1017.16.4.2020.224055 ◽

2020 ◽

Vol 16 (4) ◽

Author(s):

В. Ю. Черчель ◽

Ю. Ю. Купар ◽

М. М. Таганцова ◽

О. Ф. Стасів

Keyword(s):

Genetic Diversity ◽

Recurrent Selection ◽

State Institution ◽

Source Material ◽

The State ◽

Stress Factors ◽

Early Maturity ◽

Genetic Base ◽

Early Maturing ◽

Heterosis Breeding

Purpose. To analyze the divergence of early maturing source material of corn Zea mays L. in heterosis breeding for the genetic base formation at the State Institution the Institute of Grain Crops of the NAAS of Ukraine.Methods. Field (comprehensive assessment of morphobiological and economically valuable characteristics of the source material and maize hybrids) individual selection, cumulative and recurrent selection, backross and testcrosses breeding methods; laboratory; analysis and synthesis; statistical.Results. The results of research on the analysis of the divergence of early maturing corn source material in the conditions of the Steppe of Ukraine has become a developed harmonized working collection of corn breeding samples adapted to the stressful conditions of this region. The gradual cyclical improvement of the lines made it possible to form the core of the genetic diversity of FAO 150–290 early maturing specimens of the southern ecotype, which are competitive in heterosis breeding. The complexity of breeding for early maturity in the steppe conditions is due to the lack of material adapted to the stress factors of the South of Ukraine. The available early maturing lines of the world collection F2, F7, Ер1, Ма21, Ма23, Со125, Со255, См7, PLS61, S72, etc., were distinguished by high cold resistance, good starting plant development, intensive accumulation of dry matter during ripening, but not adapted to the deficiency of moisture in the soil and high summer temperatures. According to the results of the experiment, it was revealed that, in terms of breeding, lines of Lancaster plasma (DK427 and DK633) were the most plastic, due to which a number of new mid-early lines were obtained, for example DK2/427, DK267, DK266/417, DK633/266, DK296, etc., which were included in the registered hybrids. Formation of the genetic base of early maturing maize source material for heterosis breeding and systematization according to different breeding characteristics provided a balance of samples of alternative components, which will be further used to model heterosis hybrids in the early maturing group.Conclusions. The updated basic collection of lines is represented by the samples of plasma Iodent: DK744SVZM, DK216SVZM, DK4173SVZM, DK235zS, DK257zM, SV, DK365SVZM, DK777ZMSV, DK733-7zM,SV, DK315SVZM; Lancaster: DK296zS,VM, DK633/266zS,VM, DK2965ZSZM, DK2953 ZSZM, DK3023 ZSZM, DK236zS,ZM; Raid (SSS): DK232MV, DK2323MV, DK239MV; Mixed: DK253ZSZM, DK273MV, DK272zS, DK281SV, DK233zM,SV, DK959MV, DK9527 ZSZM, DK247MV, DK2442MV, which is the basis of the genetic diversity of early ripening corn samples included in the State register of plant varieties suitable for dissemination in Ukraine.

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Microsatellite-based characterization of cotton genotypes for verticillium wilt and fiber quality traits

Turkish Journal of Biochemistry ◽

10.1515/tjb-2017-0169 ◽

2017 ◽

Vol 43 (3) ◽

pp. 277-288

Author(s):

Amna Saeed ◽

Eminur Elçi

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Verticillium Wilt ◽

Fiber Quality ◽

Stress Factors ◽

Quality Traits ◽

Cotton Yield ◽

Fiber Quality Traits ◽

Resistant Cultivars ◽

Cotton Genotypes

Abstract Cotton (Gossypium hirsutum L.) is the most important natural textile fiber crop grown worldwide. Several biotic and abiotic stress factors affect cotton yield due to lower genetic diversity for the traits of particular interest. Verticillium wilt (VW) is one of the major factors incurring huge cotton yield losses. The most effective management option against VW is the development of resistant cultivars. The resistant cultivars must also have superior fiber quality and yield traits. Therefore, the current study was aimed at screening some of the identified simple sequence repeats (SSR) markers for VW resistance and fiber quality traits of cotton genotypes in Turkey. Fifty different cultivars were screened with 30 SSR markers. Polymerase chain reaction (PCR) was conducted to amplify the SSR markers. The amplified bands were scored as 0 or 1 for absence and presence, respectively. For the molecular data analysis, polymorphism information content (PIC) values of molecular markers were calculated. Among tested SSR markers 13 were found polymorphic, which produced a total of 677 loci. The number of alleles per marker ranged from 1 to 4 and, overall average PIC values of markers ranged from 0.00 to 0.76, respectively. Principal component analysis executed on presence absence data yielded two distinct groups of cultivars screened. Hierarchical clustering revealed low genetic diversity among the tested cultivars. Based on the results TamcotCamdES, Gloria, Natalia, Lydia, Teks, Tamcot SP37H, N87 and BA525 are the promising cultivars for further breeding studies. The results of the current study also revealed that 4 SSR markers (DPL752 and DPL322 for fiber traits, DPL0022 and GH215 for VW resistance) out of 30 could be used for improving VW resistance and fiber quality in cotton through marker assisted selection.

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Genetic diversity of mungbean (Vigna radiata L.) germplasm in Indonesia

Plant Genetic Resources ◽

10.1017/s1479262114000343 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S91-S94 ◽

Cited By ~ 7

Author(s):

Puji Lestari ◽

Sue Kyung Kim ◽

Reflinur ◽

Yang Jae Kang ◽

Nurwita Dewi ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Vigna Radiata ◽

Diversity Index ◽

Polymorphic Information Content ◽

Conservation Strategy ◽

Low Genetic Diversity ◽

Breeding Programmes ◽

The Mean ◽

Simple Sequence

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

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The efficiency of AFLP and SSR markers in genetic diversity estimation and gene pool classification of common bean (Phaseolus vulgaris L.)

Acta agriculturae Slovenica ◽

10.2478/v10014-008-0009-2 ◽

2008 ◽

Vol 91 (1) ◽

Cited By ~ 15

Author(s):

Marko Maras ◽

Jelka Šuštar-Vozlič ◽

Branka Javornik ◽

Vladimir Meglič

Keyword(s):

Genetic Diversity ◽

Phaseolus Vulgaris ◽

Common Bean ◽

Ssr Markers ◽

Gene Pool ◽

Phaseolus Vulgaris L

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Molecular Characterization of Kiwifruit (Actinidia) Cultivars and Selections Using SSR Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.3.0374 ◽

2004 ◽

Vol 129 (3) ◽

pp. 374-382 ◽

Cited By ~ 33

Author(s):

Yiqi Zhen ◽

Zuozhou Li ◽

Hongwen Huang ◽

Ying Wang

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Ssr Markers ◽

Rapd Markers ◽

Reliable Method ◽

Cultivar Identification ◽

Direct Count ◽

Polymorphic Loci ◽

Single Genotype

Forty-eight kiwifruit cultivars and selections, representing more than 90% of total world kiwifruit production, were investigated using nine SSR markers to establish genetic identities, and evaluate genetic diversity and relatedness. These nine SSRs were polymorphic and a total of 213 alleles were detected, resulting in a mean number of 23.7 alleles per locus, ranging from nine to 38 alleles. One hundred and thirty-three alleles were found to be common to both A. chinensis and A. deliciosa, while 33 and 36 were specific to A. chinensis and A. deliciosa, respectively. In addition, 34 alleles were specific to one single genotype and provided a set of valuable alleles for cultivar identification. A single SSR locus UDK 96-414 could differentiate all 48 genotypes except two presumable clones. Mean number of alleles per locus (A), percentage of polymorphic loci (P), and direct count heterozygosity (Ho) assessed for each genotype over all loci revealed considerable differences among these 48 genotypes. On average, A = 2.6, P = 89.4% and Ho = 0.546 were found in A. chinensis cultivars, while A = 3.5, P = 97.0% and Ho = 0.671 in A. deliciosa cultivars. Consensus fingerprint profiling using SSR markers is a useful and reliable method for establishing genetic identities of kiwifruit cultivars and selections. It also improves evaluation effectiveness of genetic diversity and relatedness compared to RAPD markers.

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