DNA marker characterization for allele mining of blast and bacterial leaf blight resistant genes and evaluation for grain yield

Landraces of rice were evaluated for blast and bacterial leaf blight (BLB) resistance, via tightly linked SSR markers and by phenotyping for flowering time, maturity and grain yield. Correlation between flowering maturity and grain yield was carried out using 162 local landraces and traditional rice cultivars. Days for 50% flowering ranged from 59 to 157 days, maturity from 93 to 192 days and seed yield per plant ranged from 0.24 to 33.3 g. Strong association was observed between flowering time and maturity time. Marker RG64 linked to Pi-2, a major dominant blast resistance gene on Chromosome 6 and marker pTA248 on Chromosome 11 linked to Xa21, a resistant gene to bacterial leaf blight were used to detect the presence of resistant alleles. Three different types of bands of 1 kb carrying Xa21 resistant allele and two susceptible alleles of 700 and 750 bp were amplified using pTA248. 14 rice genotypes were resistant for BLB, 46 genotypes showed susceptible banding pattern, and 87 genotypes were in heterozygous condition for resistance. 28 genotypes carried resistant alleles for both blast and bacterial leaf from among them Gowri Sanna, Ponni, Antharsali and Doddabyranellu were popularly preferred by the farmers. These can serve as donor lines for transferring of both resistances simultaneously.Keywords: Landraces, blast, bacterial leaf blight, grain yield, DNA markersAfrican Journal of Biotechnology Vol. 12(18), pp. 2331-234

Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

Figure S1. Examples of scanned root images from individual plants. Figure S2. Concatenated split network tree for the collection of 233 accessions based on 6019 SNP markers. Figure S3. LD pattern along the individual chromosomes of barley. Figure S4. Schematic representation of the eight re-sequenced candidate genes models. (DOCX 3427 kb

Non-Invasive Phenotyping Reveals Genomic Regions Involved in Pre-Anthesis Drought Tolerance and Recovery in Spring Barley

With ongoing climate change, drought events are becoming more frequent and will affect biomass formation when occurring during pre-flowering stages. We explored growth over time under such a drought scenario, via non-invasive imaging and revealed the underlying key genetic factors in spring barley. By comparing with well-watered conditions investigated in an earlier study and including information on timing, QTL could be classified as constitutive, drought or recovery-adaptive. Drought-adaptive QTL were found in the vicinity of genes involved in dehydration tolerance such as dehydrins (Dhn4, Dhn7, Dhn8, and Dhn9) and aquaporins (e.g. HvPIP1;5, HvPIP2;7, and HvTIP2;1). The influence of phenology on biomass formation increased under drought. Accordingly, the main QTL during recovery was the region of HvPPD-H1. The most important constitutive QTL for late biomass was located in the vicinity of HvDIM, while the main locus for seedling biomass was the HvWAXY region. The disappearance of QTL marked the genetic architecture of tiller number. The most important constitutive QTL was located on 6HS in the region of 1-FEH. Stage and tolerance specific QTL might provide opportunities for genetic manipulation to stabilize biomass and tiller number under drought conditions and thereby also grain yield.Peer Reviewe

Genomic Approaches to Using Diversity for the Adaptation of Modern Varieties of Wheat and Barley to Climate Change

Plant genetic resources have contributed to the identification and characterization of key loci and genes for important agronomic traits such as flowering time, plant height, root and shoot growth and resistance to abiotic stresses. Key loci for pre-anthesis growth vigor and drought tolerance have been revealed by genome-wide mapping in three diverse barley panels. Recent studies have identified candidate loci for biomass and/or the corresponding growth rates, water use efficiency, root traits, tiller number, plant height under drought or/and well-watered conditions using destructive and non-invasive 48phenotyping. In all three panels, 76 genomic regions were identified in at least two panels in which QTLs for growth and/or drought tolerance cluster, some marker-trait associations were even found for identical SNPs in all panels. The main genomic regions identified in three different mapping panels for trait complexes such as growth vigor, root architecture and pre-anthesis drought tolerance are highly relevant for future research on adaptation to climate change

Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

Background: Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits. Results: A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stressspecific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate. Conclusions: This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.This articlel is published as Abdel-Ghani, Adel H., Rajiv Sharma, Celestine Wabila, Sidram Dhanagond, Saed J. Owais, Mahmud A. Duwayri, Saddam A. Al-Dalain et al. "Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage." BMC plant biology 19 (2019): 216. doi: 10.1186/s12870-019-1828-5.</p

Evolution of the grain dispersal system in barley

SummaryAbout 12,000 years ago in the Near East, humans began the transition from hunter-gathering to agriculture-based societies. Barley was a founder crop in this process, and the most important steps in its domestication were mutations in two adjacent, dominant, and complementary genes, through which grains were retained on the inflorescence at maturity, enabling effective harvesting. Independent recessive mutations in each of these genes caused cell wall thickening in a highly specific grain “disarticulation zone,” converting the brittle floral axis (the rachis) of the wild-type into a tough, non-brittle form that promoted grain retention. By tracing the evolutionary history of allelic variation in both genes, we conclude that spatially and temporally independent selections of germplasm with a non-brittle rachis were made during the domestication of barley by farmers in the southern and northern regions of the Levant, actions that made a major contribution to the emergence of early agrarian societies