Assessment of genetic diversity in Brazilian barley using SSR markers

Genetic diversity and population structure analyses in barley (Hordeum vulgare) against corn-leaf aphid, Rhopalosiphum maidis (Fitch)

Corn-leaf aphid (CLA), Rhopalosiphum maidis (Fitch) (Hemiptera: Aphididae) is a serious economic pest of barley worldwide. Breeding for aphid resistance in plants is considered a cost-effective and environmentally safe approach for aphid control, compared to the use of chemical pesticides. One of the challenges in breeding for aphid resistance is the identification of resistant plant genotypes, which can be achieved through the use of molecular markers. In the present study, a set of aphid specific 10 simple-sequence repeats (SSR) markers were used to investigate genetic diversity and population structure analyses in 109 barley genotypes against R. maidis. Three statistical methods viz., multivariate hierarchical clustering based on Jaccard's similarity coefficient, principal coordinate analysis (PCoA) and the Bayesian approach were utilized to classify the 109 barley genotypes. The analyses revealed four subpopulations i.e., SubPop1, SubPop2, SubPop3 and SubPop4 with 19, 46, 20 and 24 genotypes including admixtures, respectively and represented 17.43%, 42.2%, 18.34% and 22.01% genotypes of the total population size, respectively. The studied SSR markers produced 67 polymorphic bands, with an average of 6.7 and ranging from 3 to 12 bands. Heterozygosity (H) was found to be highest in SSR28 (0.64) and lowest in SSR27 (0.89). The observed genetic diversity index varied from 0.10 to 0.34 (with an average of 0.19). Major allele frequency varied from 74.08% to 94.80%. On an average, 87.52% of the 109 barley genotypes shared a common major allele at any locus. Based on the Aphid Infestation Index (AII), only 2 genotypes were found to be resistant against CLA. SubPop2 also had lowest mean aphid population (28.83), widest genetic similarity index (0.60-1.00) and highest genetic similarity coefficient (0.82), which highlighted its potential for inclusion in future CLA resistance breeding programs.

Molecular Evaluation and Identification of Some Barley Hybrids Tolerant to Salt Stress

<b>Background and Objective:</b> Barley is considering one of the most important cereal crops at the local and global levels. It is ranked second in terms of nutritional importance after wheat and its flour contributes significantly to bridging the large nutritional gap in the production of Egyptian bread. The aim of this study concentrated on knowing and testing the genetic behaviour responsible for salinity stress tolerance in barley as trying to improve barley crop and increase its ability for abiotic stress resistance under Egyptian conditions. <b>Materials and Methods:</b> Twenty-one crosses and ten parents of barley with different responses to salinity tolerance were evaluated in this investigation under normal and salinity conditions. Yield and its components and some physiological traits related to salt stress tolerance were the most important studied attributes evaluated in this regard under both conditions. Moreover, SSR markers were used to evaluate and identified associated markers for salinity tolerance in selected hybrids and comparing among the ten barley parents. <b>Results:</b> The final results confirmed that the three testers; Giza 123, Giza 126 and Giza 2000 besides; the crosses; Line 1XTester 1 (Giza 125XGiza 123), Line 2XTester 1 (Giza 133XGiza 123), Line 1XTester 2 (Giza 125XGiza 126), Line 2XTester 2 (Giza 133XGiza 126) and Line 1XTester 3 (Giza 125XGiza 2000) exhibited highly salinity tolerance under saline stress treatment compared with the control experiment. Among 15 analyzed barley entries, the chosen set of 11 markers amplified 20 alleles with an average of 1.81, with a range from 1-4 alleles. <b>Conclusion:</b> The results of SSR analysis and the data on valued agricultural trait loci determined the genetic distance among parents and their hybrids, which is of an unlimited rate for breeders.

Protocol development for somatic embryogenesis, SSR markers and genetic modification of Stipagrostis pennata (Trin.) De Winter

BACKGROUND

Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources.

RESULTS

A protocol for plant regeneration from somatic embryos of S. pennata was developed. Somatic embryogenesis was induced on Murashige & Skoog (MS) medium supplemented with 3 mg·L-1 2,4-D subsequently shoots were induced on MS medium and supplemented with 5 mg·L-1 zeatin riboside. The highest shoots induction was obtained when embryogenic callus derived from mature embryos (96%) in combination with MS filter-sterilized medium was used from Khuzestan location. The genetic stability of regenerated plants was analysed using ten simple sequence repeats (SSR) markers from S. pennata which showed no somaclonal variation in regenerated plants from somatic embryos of S. pennata. The regenerated plants of S. pennata showed genetic stability without any somaclonal variation for the four pairs of primers that gave the expected amplicon sizes. This data seems very reliable as three of the PCR products belonged to the coding region of the genome. Furthermore, stable expression of GUS was obtained after Agrobacterium-mediated transformation using a super binary vector carried by a bacterial strain LBA4404.

CONCLUSION

To our knowledge, the current work is the first attempt to develop an in vitro protocol for somatic embryogenesis including the SSR marker analyses of regenerated plants, and Agrobacterium-mediated transformation of S. pennata that can be used for its large-scale production for commercial purposes.

Content analysis of vitamins, dietary fibers and amino acids in a wide collection of barley (Hordeum vulgare L.) from Tibet, China

Barley (Hordeum vulgare L.) is an important agricultural crop. Various studies on the genetic diversity, biochemical and molecular attributes on this species are known. However, information on nutritional variability in a large panel of barley cultivars is limited. Therefore, it is of interest for a quantitative analysis of vitamins, amino acids and dietary fibers in 245 barley of Tibet region in China. The coefficient of variation analysis revealed strong variation of vitamins (VB1>VB2>VE), essential amino acids (valine, histidine, methionine, lysine), non-essential amino acids (proline, tyrosine, cysteine), dietary fibers, (cellulose > lignin). Principal component analysis detected three clusters of cultivars, each with specific characteristics. However, the most nutritional cultivars were found in Cluster 3, which encompassed 52 cultivars. Distinctly, six cultivars (ZQ2000, BJX230, BJX229, BJX249, BJX191 and BJX265) were identified with highest nutritional values. This study reveals a large nutritional diversity in barley cultivars from Tibet and represents an important reference for the exploitation of these germplasm in crop improvement and breeding programmes.

Assessment of phenotypic and storage protein diversity in exotic barley cultivated in District Dir (Pakistan)

A total of 198 exotic barley genotypes were collected from the Gene Bank of the Plant Genetic Resource Institute (PGRI), National Agriculture Research Center (NARC), Islamabad, Pakistan, for the assessment of genetic diversity based on morphological and seed storage proteins. Qualitative and quantitative traits were noted as per IPGRI, 1994 descriptor. Among the quantitative parameters, a high level of genetic variability index was noted in seeds per spike at 79.9% of coefficient of variance followed by biomass per plant which shows 37.4% variance, while minimum variance in quantitative traits was noted in days to germination at 5.4% followed by days to maturity at 3.1% with average mean genetic variation in all quantitative traits at 97.6%. Assay of total seed protein in these exotic accessions was analogue through polyacrylamide gel electrophoresis. A high level of variation was noted in loci (bands) B26 (0.98%) followed by B25 (0.89%), B24 (0.78%),B23 (0.69%) and B01 (0.52%). A similarly low level of variation was detected in B03 (0.16%) followed by B06 (0.18%), B13 (0.19%), B12 (0.21%), B11 (0.23%), B05 (0.24%), B07 (0.25%), B21 (0.34%), B20 (0.35%), B17 (0.39%). The results indicate that the mean value of variation in these accessions is 97.6%. Further assessments and exploration were suggested for these genotypes in multi-climatic zones to satisfy farmers’ need, breeders’ interest and malt-industrial requirements.

Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis

Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.

Genetic Variation and Alleviation of Salinity Stress in Barley (Hordeum vulgare L.)

Barley (Hordeum vulgare L.) represents one of the most important cereals cultivated worldwide. Investigating genetic variability and structure of barley is important for enhancing the crop productivity. This study aimed to investigate the diversity and structure of 40 barley genotypes originated from three European countries (France, the Netherlands, Poland) using amplified fragment length polymorphisms (AFLPs). It also aimed to study 5-aminolevulinic acid (ALA) effect on salinity tolerance of six barley genotypes. The expected heterozygosity (H_e) diverged from 0.126 to 0.501, with a mean of 0.348. Polymorphic information content (PIC) diverged from 0.103 to 0.482 across barley genotypes, with a mean of 0.316, indicating that barley genotypes are rich in a considerable level of genetic diversity. The 40 barley genotypes were further studied based on their geographical origin (Western Europe and Eastern Europe). The Eastern European region (Poland) has a higher barley variability than the Western European region (France and the Netherlands). Nei’s distance-based cluster tree divided the 40 barley accessions into two major clusters; one cluster comprised all the varieties originated from the Eastern European region, while the other major cluster included all accessions originated from the Western European region. Structure analysis results were in a complete concordance with our cluster analysis results. Slaski 2, Damseaux and Urbanowicki genotypes have the highest diversity level, whereas Carmen, Bigo and Cambrinus genotypes have the lowest level. The response of these six varieties to NaCl stress was also investigated. Salt stress (100 mM NaCl) slightly decreased levels of chlorophyll, carotenoid and osmolytes (proteins, soluble sugars, phenolics and flavonoids) in the leaves of Slaski 2, Damseaux and Urbanowicki genotypes at non-significant level, as compared to control samples. However, pigment contents and osmolytes in leaves of Carmen, Bigo and Cambrinus genotypes were significantly decreased by salt stress. Antioxidant enzyme activities were significantly increased in Slaski 2 genotype, but non-significantly increased in Carmen by salt stress. Priming Slaski 2 and Carmen cultivars with ALA under salt stress significantly induced pigment contents, antioxidants enzymes activity and stress-responsive genes expression, relative to NaCl-stressed plants. In conclusion, this study suggested a correlation between variability percentage and degree of salinity resistance. ALA improved salt tolerance in barley.

Is a non-synonymous SNP in the HvAACT1 coding region associated with acidic soil tolerance in barley?

The barley HvAACT1 gene codes for a citrate transporter associated with tolerance to acidic soil. In this report, we describe a single nucleotide polymorphism (SNP) in the HvAACT1 coding region that was detected as T-1,198 (in genotypes with lower root growth on acidic soil) or G-1,198 (greater root growth) and resulted in a single amino acid change (L/V-172). Molecular dynamic analysis predicted that HvAACT1 proteins with L or V-172 were stable, although the substitution led to structural changes within the protein. To evaluate the effect of the SNP on tolerance to acidic soil, barley accessions were separated into haplotypes based on the presence of a 1 kb insertion in the HvAACT1 promoter and a 21 bp insertion/deletion. These markers and the SNP-1,198 allowed the identification of five haplotypes. Short-term soil experiments showed no difference in root growth for most of the accessions containing the 21 bp insertion and T or G-1,198. In contrast, genotypes showing both the 21 bp deletion and G-1,198, with one of them having the 1 kb insertion, showed greater root growth. These results indicate that the SNP was not advantageous or deleterious when genotypes from the same haplotype were compared. The occurrence of the SNP was highly correlated with the 21 bp insertion/deletion that, together with the 1 kb insertion, explained most of the barley tolerance to acidic soil.