Assessment of genetic diversity in the sorghum reference set using EST-SSR markers

Ramu, Punna; Billot, Claire; Rami, Jean-François; Senthilvel, S.; Upadhyaya, Hari D.; Reddy, L. Ananda; Hash, C. Tom

doi:10.1007/s00122-013-2117-6

Cited by 81 publications

(77 citation statements)

References 76 publications

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“…Therefore, SSRs have increasingly become the marker set of choice for genetic studies as they are abundant, highly polymorphic, codominant in nature, and genome-specific (Cuevas and Prom, 2013;Izzah et al, 2013). Being so important, SSR markers were previously used for assessing genetic diversity in pea (Taran et al, 2005;Nasiri et al, 2009), but anonymous SSRs are more costly and time-consuming to develop from genomic libraries (Ramu et al, 2013). An alternate to SSR markers is to develop expressed sequence tag (EST)-based SSRs through available EST databases (Simko, 2009).…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of edible pea through EST-SSR markers

Nisar¹,

Khan²,

Wadood³

et al. 2017

Turk J Bot

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Section: Introductionmentioning

confidence: 99%

Molecular characterization of edible pea through EST-SSR markers

Nisar¹,

Khan²,

Wadood³

et al. 2017

Turk J Bot

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“…The genotype grouping observed in the current study followed racial based classification, in line with previous reports (e.g. Deu et al, 2006;Ramu et al, 2013). The majority of the landrace genotypes predominantly adapted to highland (90%), intermediate (79%) and lowland (55%) agro-ecological zones of durra racial type grouped in cluster I along with a small number of bicolor racial types.…”

Section: Genome Wide Differentiation Detected Within and Among Sorghusupporting

confidence: 91%

“…A similar result has been reported using RFLP markers (Deu et al, 2006). Genetic variability and the genetic basis of racial classifications in sorghum have also been studied using different types of DNA based markers (Brown et al, 2011;Morris et al, 2013;Perumal et al, 2007;Ramu et al, 2013). Previous studies have been reflected the correspondence between the racial classifications based on morphological traits and the grouping of sorghum genotypes based molecular marker based genetic distance which also reflected the geographical distribution of sorghum, with the exception of the bicolor race (Brown et al, 2011;Deu et al, 2006;Perumal et al, 2007).…”

Section: Sorghum Genetic Variability In a Global Contextsupporting

confidence: 59%

“…Despite the wider use of the concept of heterosis for hybrid development, there is no clear Previous studies analyzing genetic diversity in the sorghum gene-pool have shown a high degree of correspondence between sorghum racial classification and marker-based grouping (Brown et al, 2011;Ramu et al, 2013). To date, a number of studies have also been conducted on sorghum germplasm from Ethiopia using limited numbers of molecular markers, e.g.…”

Section: 2introductionmentioning

confidence: 99%

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Genetic differentiation, heterotic performance and grain yield determinate traits of locally adapted sorghum genotypes in contrasting environments in Ethiopia

Mindaye¹

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The increase superiority in characteristics such as size, growth rate, fertility, yield and general fitness of hybrids produced by crossing genetically diverse inbred parents is well established in many plant and animal species. This phenomenon has been exploited to produce commercial cultivars in a range of crop species including sorghum.In sorghum F1 hybrid seed is produced by crossing genetically distinct restorer (R lines) and cytoplasmic male sterile seed parent (A lines). In the developed world commercial cultivars are almost exclusively F1 hybrids and are increasingly being used in the developing countries. In spite of the yield advantage in some circumstances, however, hybrids developed using introduced parental lines have not been adopted by Ethiopian farmers primarily because of the extra cost of purchasing seed has not been outweighed by the benefits of introduced hybrids in particular the lack of farmer preferred traits such as tall stature and larger grain size. The development of hybrids using locally adapted genotypes could have the potential to overcome the shortcomings of introduced hybrids. However, the complex cytoplasmic male sterility system and prevalence of restorer genes complicate the development of new Additionally, the hybrids derived from these locally adapted genotypes will have the benefit of containing farmers preferred traits. The groups most divergent from the introduced A/B lines were the Ethiopian landraces adapted to highland and intermediate agro-ecologies and a subset of lowland adapted genotypes. These genotype groups were also grouped distinctly from the introduced R lines, and hence provide highly divergent parental lines for hybrid development in Ethiopia.The performance and magnitude of heterosis of 139 F1 hybrids, derived from introduced seed parents crossed with selected locally adapted genotypes and introduced R lines, were evaluated in three contrasting environments. The lowland adapted hybrids displayed a mean better parent heterosis (BPH)iii of 19% and a 29% increase in grain yield, on average, in comparison to the hybrids derived from the introduced R lines. In addition, these hybrids were also found to be superior in plant height and grain weight. The mean BPH for grain yield for the highland adapted hybrids was 16% in the highland and 52 % in the intermediate, in addition to increased grain weight. The magnitude of heterosis between the three hybrid groups reflected the genetic distance between the genotype groups with the A/B lines.These results highlight the potential of locally adapted genotypes for the exploitation of heterosis in Ethiopia.In order to understand the genetic basis of increased hybrid performance, the relationship between yield component traits was assessed and the genetic variance for each subset of hybrid group was partitioned into parental lines and their interaction effects. In the lowland environment, increase in grain number and grain weight contributed to increased yield of the lowland adapted hybrids in comparison to the intro...

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“…ESTs are short transcribed sequences that have permitted the development of SSR markers in several species of plants (Gadaleta et al, 2011;Kumari et al, 2013;Şelale et al, 2013;Zhang et al, 2014;Ju et al, 2015). This has resulted in the subsequent identification of genetic diversity through the use of EST-SSR markers (Mujaju et al, 2013;Ramu et al, 2013;Malfa et al, 2014). Although Jerusalem artichoke is an important crop with both economic and cultural significance, very few informative molecular markers have been isolated from its genome.…”

Section: Introductionmentioning

confidence: 99%

Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.)

Mornkham¹,

Wangsomnuk²,

Mo³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Jerusalem artichoke (Helianthus tuberosus L.) is a perennial tuberous plant and a traditional inulin-rich crop in Thailand. It has become the most important source of inulin and has great potential for use in chemical and food industries. In this study, expressed sequence tag (EST)-based simple sequence repeat (SSR) markers were developed from 40,362 Jerusalem artichoke ESTs retrieved from the NCBI database. Among 23,691 non-redundant identified ESTs, 1949 SSR motifs harboring 2 to 6 nucleotides with varied repeat motifs were discovered from 1676 assembled sequences. Seventy-nine primer pairs were generated from EST sequences harboring SSR motifs. Our results show that 43 primers are polymorphic for the six studied populations, while the remaining 36 were either monomorphic or failed to amplify. These 43 SSR loci exhibited a high level of genetic diversity among populations, with allele numbers varying from 2 to 7, with an average of 3.95 alleles per loci. Heterozygosity ranged from 0.096 to 0.774, with an average of 0.536; polymorphic index content ranged from 0.096 to 0.854, with an average of 0.568. Principal component analysis and neighbor-joining analysis revealed that the six populations could be divided into six clusters. Our results indicate that these newly characterized EST-SSR markers may be useful in the exploration of genetic diversity and range expansion of the Jerusalem artichoke, and in cross-species application for the genus Helianthus.

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Assessment of genetic diversity in the sorghum reference set using EST-SSR markers

Cited by 81 publications

References 76 publications

Molecular characterization of edible pea through EST-SSR markers

Molecular characterization of edible pea through EST-SSR markers

Genetic differentiation, heterotic performance and grain yield determinate traits of locally adapted sorghum genotypes in contrasting environments in Ethiopia

Development and characterization of novel EST-SSR markers and their application for genetic diversity analysis of Jerusalem artichoke (Helianthus tuberosus L.)

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