A study of genetic diversity of colored barley (Hordeum vulgare L.) using SSR markers

Hua, Wei; Zhang, Xiaoqin; Zhu, Jianfeng; Shang, Yi; Wang, Junmei; Jia, Qiaojun; Li, Chengdao; Yang, Jianming

doi:10.1007/s10722-014-0165-7

Cited by 23 publications

(12 citation statements)

References 33 publications

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“…They are widely distributed throughout the genomes in both coding and non-coding regions; they are codominant, multi-allelic, chromosome specific and highly informative genetic markers (Cho et al 2000 ; Scott et al 2000 ). They are amenable to high throughput genotyping, thus suitable for diversity analysis (Hua et al 2015 ; Wang et al 2011 ). The SSR markers have been used successfully for the evaluation of genetic diversity among several species, including finger millet (Babu et al 2014b ), foxtail millet (Kim et al 2012 ; Zhao et al 2012 ) and proso millet (Cho et al 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers

Ramakrishnan¹,

Ceasar

Duraipandiyan

et al. 2016

SpringerPlus

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We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60–70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard’s similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard’s similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on their geographic regions.

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Section: Introductionmentioning

confidence: 99%

Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers

Ramakrishnan¹,

Ceasar

Duraipandiyan

et al. 2016

SpringerPlus

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“…This grain is mainly used as feed, as food for human, and for brewing beer (Mayer et al 2012). The nutritional value of barley has increasingly attracted considerable attention because of its high dietary fiber and valuable b-glucan's contents (Hua et al 2015). Barley has superior tolerance to drought, salinity, aluminum, and other abiotic stresses over most other cereal crops (Dai et al 2013;Ahmed et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis of barley (Hordeum vulgare L.) glossy mutant using RNA-Seq

Luan¹,

Shen²,

Zhang³

et al. 2016

Braz. J. Bot

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Waxy cuticle plays an important role in the resistance to various biotic and abiotic stresses. Barley is generally covered with cuticular wax, but glossy mutants are shiny green without wax. The morphological structure of wax was found to be significantly different between the glossy mutant and the wild-type line when examined under a scanning electron microscope. Transcriptomic analysis was performed to identify genes related to waxy cuticle formation. A total of 243 differentially expressed genes (DEGs) were detected. Seven unigenes related to waxy cuticle biosynthesis were confirmed by quantitative realtime PCR. Results were highly consistent with the RNA-Seq results. Differential expressions of WAX2, WSD1, FAR1, and LACS could potentially explain the differences in the cuticular waxes of the two barley lines. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway-enrichment analyses were performed to better understand the functions of these DEGs. This study not only provides valuable information for understanding the molecular mechanisms of the synthesis of cuticular waxes and metabolism, but also establishes the foundations for further genomics research and waxy gene cloning in barley.

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“…SSR markers have been extensively used in barley genetic diversity (Elakhdar et al, 2016a;Ferreira et al, 2016;Elakhdar et al, 2018;Arya et al, 2019), Association mapping (Jamali et al, 2017) linkage mapping and phylogenetic analysis (Lakew et al, 2013;Zhang et al, 2014). Among different DNA marker types used in barley, microsatellites have proven to be the markers of choice for genetic diversity studies for this plant species (Wang et al, 2010;Hua et al, 2015;Todorovska et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Diversity Maintenance of Some Barley (Hordeum Spp) Genetic Resources Using SSR-Based Marker

2020

THE JAPS

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Barley is an important cereal crop cultivated in many parts of the world since ancient times. Genetic diversity was studied in a set of 16 barley (Hordeum spp) genotypes using 25 microsatellite (SSR) loci. A total of 94 different alleles distributed over all the seven chromosomes of barley. Out of these, 76 alleles were polymorphic with an average of 3.04 alleles/primer. Major allele frequency, gene diversity and PIC were estimated based on allele frequencies, having the mean values of 0.543, 0.571 and 0.513, respectively. Principal component analysis indicated the presence of high genetic variability among barley genotypes. ATACO, Canela, Local Abiad Sulaimani and Amal2 were identified to be highly distanced from other genotypes. The dendrogram created by hierarchical cluster analysis using the UPGMA algorithm was able to discriminate the genotypes into 7 groups according to their genetic distance. Both analyses parallel to principal coordinate analysis are indicating the close relatedness between Quinn, Zanbaka, Al-khair and Arta/3/Avar genotypes that exchange genetic material through continuous previous breeding programs. These values indicate high differentiation ability of SSR markers for genetic studies in barley and their utility for barley genetics and breeding.

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A study of genetic diversity of colored barley (Hordeum vulgare L.) using SSR markers

Cited by 23 publications

References 33 publications

Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers

Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers

Comparative transcriptome analysis of barley (Hordeum vulgare L.) glossy mutant using RNA-Seq

Diversity Maintenance of Some Barley (Hordeum Spp) Genetic Resources Using SSR-Based Marker

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