Chromosome 2H Research Articles

Major Susceptibility Gene Epistasis over Minor Gene Resistance to Spot Form Net Blotch in a Commercial Barley Cultivar.

Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant global disease of barley (Hordeum vulgare). Baudin, a barley cultivar that was until recently extensively grown in Western Australia, was reported as having minor seedling resistance. However, Baudin was highly susceptible to a local isolate, M3, suggesting that this isolate had gained virulence against a major susceptibility gene. M3 causes atypical lesions with pale centers early in the infection, with initial screens of a segregating population indicating that this was determined by a single locus in the Baudin genome. The susceptibility was semidominant in F1 progeny and the susceptibility gene, designated Spm1 (Susceptibility to P. teres f. maculata 1), mapped to a 190-kb section of the resistance gene-rich Mla region of chromosome 1H. Phenotyping with Ptm SP1, a non-M3 pathotype, identified a seedling resistance locus on 2H. Minor gene resistance is generally regarded as potentially durable, but our findings suggest the resistance to spot form net blotch in Baudin is nullified by strong susceptibility conferred by a separate locus on 1H. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley.

Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.

Conjunctive Analyses of BSA-Seq and BSR-Seq to Identify Candidate Genes Controlling the Black Lemma and Pericarp Trait in Barley.

Black barley seeds are a health-beneficial diet resource because of their special chemical composition and antioxidant properties. The black lemma and pericarp (BLP) locus was mapped in a genetic interval of 0.807 Mb on chromosome 1H, but its genetic basis remains unknown. In this study, targeted metabolomics and conjunctive analyses of BSA-seq and BSR-seq were used to identify candidate genes of BLP and the precursors of black pigments. The results revealed that five candidate genes, purple acid phosphatase, 3-ketoacyl-CoA synthase 11, coiled-coil domain-containing protein 167, subtilisin-like protease, and caffeic acid-O-methyltransferase, of the BLP locus were identified in the 10.12 Mb location region on the 1H chromosome after differential expression analysis, and 17 differential metabolites, including the precursor and repeating unit of allomelanin, were accumulated in the late mike stage of black barley. Phenol nitrogen-free precursors such as catechol (protocatechuic aldehyde) or catecholic acids (caffeic, protocatechuic, and gallic acids) may promote black pigmentation. BLP can manipulate the accumulation of benzoic acid derivatives (salicylic acid, 2,4-dihydroxybenzoic acid, gallic acid, gentisic acid, protocatechuic acid, syringic acid, vanillic acid, protocatechuic aldehyde, and syringaldehyde) through the shikimate/chorismite pathway other than the phenylalanine pathway and alter the metabolism of the phenylpropanoid-monolignol branch. Collectively, it is reasonable to infer that black pigmentation in barley is due to allomelanin biosynthesis in the lemma and pericarp, and BLP regulates melanogenesis by manipulating the biosynthesis of its precursors.

Genome diversity and highland-adaptative variation in Tibet barley landrace population of China.

Barley landraces accumulated variation in adapting to extreme highland environments during long-term domestication in Tibet, but little is known about their population structure and genomic selection traces. In this study, tGBS (tunable genotyping by sequencing) sequencing, molecular marker and phenotypic analyses were conducted on 1,308 highland and 58 inland barley landraces in China. The accessions were divided into six sub-populations and clearly distinguished most six-rowed, naked barley accessions (Qingke in Tibet) from inland barley. Genome-wide differentiation was observed in all five sub-populations of Qingke and inland barley accessions. High genetic differentiation in the pericentric regions of chromosomes 2H and 3H contributed to formation of five types of Qingke. Ten haplotypes of the pericentric regions of 2H, 3H, 6H and 7H were further identified as associated with ecological diversification of these sub-populations. There was genetic exchange between eastern and western Qingke but they shared the same progenitor. The identification of 20 inland barley types indicated multiple origins of Qingke in Tibet. The distribution of the five types of Qingke corresponded to specific environments. Two predominant highland-adaptative variations were identified for low temperature tolerance and grain color. Our results provide new insights into the origin, genome differentiation, population structure and highland adaptation in highland barley which will benefit both germplasm enhancement and breeding of naked barley.

Genetic and physical localization of a major susceptibility gene to Pyrenophora teres f. maculata in barley

Key messageGenetic characterization of a major spot form net blotch susceptibility locus to using linkage mapping to identify a candidate gene and user-friendly markers in barley.Spot form net blotch (SFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata (Ptm), is an economically important foliar diseases in barley. Although various resistance loci have been identified, breeding for SFNB-resistant varieties has been hampered due to the complex virulence profile of Ptm populations. One resistance locus in the host may be effective against one specific isolate, but it may confer susceptibility to other isolates. A major susceptibility QTL on chromosome 7H, named Sptm1, was consistently identified in many studies. In the present study, we conduct fine mapping to localize Sptm1 with high resolution. A segregating population was developed from selected F2 progenies of the cross Tradition (S) × PI 67381 (R), in which the disease phenotype was determined by the Sptm1 locus alone. Disease phenotypes of critical recombinants were confirmed in the following two consecutive generations. Genetic mapping anchored the Sptm1 gene to an ⁓400 kb region on chromosome 7H. Gene prediction and annotation identified six protein-coding genes in the delimited Sptm1 region, and the gene encoding a putative cold-responsive protein kinase was selected as a strong candidate. Therefore, providing fine localization and candidate of Sptm1 for functional validation, our study will facilitate the understanding of susceptibility mechanism underlying the barley-Ptm interaction and offers a potential target for gene editing to develop valuable materials with broad-spectrum resistance to SFNB.

ФОРМИРОВАНИЕ ПОЯСКОВ КАСПАРИ В КОРНЯХ ПОЧТИ ИЗОГЕННЫХ ЛИНИЙ ЯЧМЕНЯ, ОТЛИЧАЮЩИХСЯ НАЛИЧИЕМ МЕЛАНИНОВОЙ ОКРАСКИ КОЛОСА

The influence of the BLP locus genes, which control the formation of black coloration of the spike glumes and grain pericarp on the formation of Casparian bands in Hordeum vulgare L. plants, was studied. The experiment was carried out with plants of the Bowman variety and three almost isogenic lines obtained on its basis: the BLP line, carrying one recombinant section from the donor of the trait of black coloration of the ear; a line with a dark gray mBLP grain and a line with a light gray gBLP grain, carrying recombinant regions in chromosomes 1H, 2H, 3H. Lignin and suberin deposition were assessed on transverse sections of root tissue. Lignin and suberin on histological sections were stained with an aqueous solution of berberine hemisulfate. On the 7th day after the start of germination, on sections made in the basal part of the root, luminescence with berberine revealed no differences between plants of different genotypes in the level of accumulation of lignin and suberin. On the 10th day, on sections of the basal part of the roots of the gBLP line, staining of the radial walls of the endoderm is noticeable, which indicates the deposition of lignin in the endoderm area, characteristic of the formation of Casparian bands, as well as in the area of metaxylem vessels. Thus, it was revealed that the gBLP genotype is characterized by accelerated formation of apoplastic barriers. The Bowman and gBLP genotypes we selected, which contrast in the rate of formation of Casparian bands, are a convenient object for further identifying the relationship between the rate of formation of Casparian bands and salt tolerance of plants.

Interaction and association analysis of malting related traits in barley.

Barley is considered as a foundation of the brewing and malting industry. Varieties with superior malt quality traits are required for efficient brewing and distillation processes. Among these, the Diastatic Power (DP), wort-Viscosity (VIS), β-glucan content (BG), Malt Extract (ME) and Alpha-Amylase (AA) are controlled by several genes linked to numerous quantitative trait loci (QTL), identified for barley malting quality. One of the well-known QTL, QTL2, associated with barley malting trait present on chromosome 4H harbours a key gene, called as HvTLP8 that has been identified for influencing the barley malting quality through its interaction with β-glucan in a redox-dependent manner. In this study, we examined to develop a functional molecular marker for HvTLP8 in the selection of superior malting cultivars. We first examined the expression of HvTLP8 and HvTLP17 containing carbohydrate binding domains in barley malt and feed varieties. The higher expression of HvTLP8 prompted us to further investigate its role as a marker for malting trait. By exploring the 1000 bp downstream 3' UTR region of HvTLP8, we found single nucleotide polymorphism (SNP) in between Steptoe (feed variety) and Morex (malt variety), which was further validated by Cleaved Amplified Polymorphic Sequence (CAPS) marker assay. Analysis of 91 individuals from the Steptoe x Morex doubled haploid (DH) mapping population revealed CAPS polymorphism in HvTLP8. Highly significant (p<0.001) correlations among ME, AA and DP malting traits were observed. The correlation coefficient (r) between these traits ranged from 0.53 to 0.65. However, the polymorphism in HvTLP8 did not correlate effectively with ME, AA, and DP. Altogether, these findings will help us to further design the experiment regarding the HvTLP8 variation and its association with other desirable traits.

Поліморфізм мікросателітних локусів хромосоми 5H ячменю (Hordeum vulgare L.) і асоціації алелів з морозостійкістю

Barley (Hordeum vulgare L.) is a crop of great economic importance for many countries of the world, including Ukraine. One of the main reason limiting barley production in different regions of Ukraine is low-temperature stress. Prediction of frost resistance in the development and choice of resistant genotypes is one of the main tasks of the breeding. Applying the tools of molecular genetic analysis involves increasing the efficiency of traditional methods of identification and genotype screening with the necessary traits in a specific climatic area. The 5H chromosomal loci are a component of a complex system of genes involved in the formation of resistance to low negative temperatures. The polymorphism and allele distribution of nine microsatellite loci in chromosome 5H, which are localisation in the region of the key NT- resistance genes Fr-H1, Fr-H2 and close to these regions in 35 varieties of the autumn barley collection, were studied. Allelic polymorphism with the presence of two (UMB702) to five (Bmag0223) alleles was detected at the loci Bmag0223, Bmag0323, Bmag0760, GMS061 and UMB702. The frost resistance of 31 varieties with different durations of hardening was evaluated and essential differences between them were noted for this feature. According to the results of the analysis of polymorphism of microsatellite loci and data on evaluation of varieties for frost resistance, the connection of allelic differences of four out of five polymorphic loci with the level of frost resistance and hardening rates was revealed. Reliable associations were established between the presence of alleles Bmag0223, Bmag0323, Bmag0760, GMS061 and indicators of the level of frost resistance. Allelic differences at the UMB702 locus were not associated with differences in any of the traits. Alleles of the microsatellite locus Bmag0223 are recommended for negative choice of less frost-resistant barley genotypes at the early plant breeding stages.

Genetic resistance in barley against Japanese soil-borne wheat mosaic virus functions in the roots.

Infection by the Japanese soil-borne wheat mosaic virus (JSBWMV) can lead to substantial losses in the grain yield of barley and wheat crops. While genetically based resistance to this virus has been documented, its mechanistic basis remains obscure. In this study, the deployment of a quantitative PCR assay showed that the resistance acts directly against the virus rather than by inhibiting the colonization of the roots by the virus' fungal vector Polymyxa graminis. In the susceptible barley cultivar (cv.) Tochinoibuki, the JSBWMV titre was maintained at a high level in the roots during the period December-April, and the virus was translocated from the root to the leaf from January onwards. In contrast, in the roots of both cv. Sukai Golden and cv. Haruna Nijo, the titre was retained at a low level, and translocation of the virus to the shoot was strongly suppressed throughout the host's entire life cycle. The roots of wild barley (Hordeum vulgare ssp. spontaneum) accession H602 responded in the early stages of infection similarly to those of the resistant cultivated forms, but the host was unable to suppress the translocation of the virus to the shoot from March onwards. The virus titre in the root was presumed to have been restricted by the action of the gene product of Jmv1 (on chromosome 2H), while the stochastic nature of the infection was suppressed by the action of that of Jmv2 (on chromosome 3H), a gene harbored by cv. Sukai Golden but not by either cv. Haruna Nijo or accession H602.

Malting quality and preharvest sprouting traits are genetically correlated in spring malting barley

Key messageMalt for craft “all-malt” brewing can have high quality, PHS resistance, and malted in normal timeframes. Canadian style adjunct malt is associated with PHS susceptibility.Expansion of malting barley production into non-traditional growing regions and erratic weather has increased the demand for preharvest sprouting (PHS) resistant, high quality malting barley cultivars. This is hindered by the relatively unknown relationships between PHS resistance and malting quality. Here we present a three-year study of malting quality and germination at different after-ripening durations post physiological maturity. Malting quality traits alpha amylase (AA) and free amino nitrogen (FAN) and germination rate at six days post PM shared a common association with a SNP in HvMKK3 on chromosome 5H in the Seed Dormancy 2 (SD2) region responsible for PHS susceptibility. Soluble protein (SP) and soluble over total protein (S/T) both shared a common association with a marker in the SD2 region. Significant genetic correlations between PHS resistance and the malting quality traits AA, FAN, SP, S/T were detected across and within HvMKK3 allele groups. High adjunct malt quality was related to PHS susceptibility. Selection for PHS resistance led to a correlated response in malting quality traits. Results strongly suggest pleiotropy of HvMKK3 on malting quality traits and that the classic “Canadian-style” malt is caused by a PHS susceptible allele of HvMKK3. PHS susceptibility appears to benefit the production of malt intended for adjunct brewing, while PHS resistance is compatible with all-malt brewing specifications. Here we present our analysis on the effect of combining complexly inherited and correlated traits with contrasting goals to inform breeding practice in malting barley, the general principles of which can be extended to other breeding programs.

Characterization of Leaf Rust Resistance in International Barley Germplasm Using Genome-Wide Association Studies

A panel of 114 genetically diverse barley lines were assessed in the greenhouse and field for resistance to the pathogen Puccinia hordei, the causal agent of barley leaf rust. Multi-pathotype tests revealed that 16.6% of the lines carried the all-stage resistance (ASR) gene Rph3, followed by Rph2 (4.4%), Rph1 (1.7%), Rph12 (1.7%) or Rph19 (1.7%). Five lines (4.4%) were postulated to carry the gene combinations Rph2+9.am, Rph2+19 and Rph8+19. Three lines (2.6%) were postulated to carry Rph15 based on seedling rust tests and genotyping with a marker linked closely to this gene. Based on greenhouse seedling tests and adult-plant field tests, 84 genotypes (73.7%) were identified as carrying APR, and genotyping with molecular markers linked closely to three known APR genes (Rph20, Rph23 and Rph24) revealed that 48 of the 84 genotypes (57.1%) likely carry novel (uncharacterized) sources of APR. Seven lines were found to carry known APR gene combinations (Rph20+Rph23, Rph23+Rph24 and Rph20+Rph24), and these lines had higher levels of field resistance compared to those carrying each of these three APR genes singly. GWAS identified 12 putative QTLs; strongly associated markers located on chromosomes 1H, 2H, 3H, 5H and 7H. Of these, the QTL on chromosome 7H had the largest effect on resistance response to P. hordei. Overall, these studies detected several potentially novel genomic regions associated with resistance. The findings provide useful information for breeders to support the utilization of these sources of resistance to diversify resistance to leaf rust in barley and increase resistance durability.

A single nucleotide substitution in the MATE transporter gene regulates plastochron and the many noded dwarf phenotype in barley (Hordeum vulgare L.)

In higher plants, the shoot apical meristem produces lateral organs in a regular spacing (phyllotaxy) and timing (plastochron). The molecular analysis of mutants associated with phyllotaxy and plastochron would increase our understanding of the mechanism of shoot architecture formation. In this study, we identified mutant mnd8ynp5 that shows an increased rate of leaf emergence and a larger number of nodes in combination with a dwarfed growth habit from an EMS-treated population of the elite barley cultivar Yangnongpi 5. Using a map-based cloning strategy, the mnd8 gene was narrowed down to a 6.7-kb genomic interval on the long arm of chromosome 5H. Sequence analysis revealed that a C to T single-nucleotide mutation occurred at the first exon (position 953) of HORVU5Hr1G118820, leading to an alanine (Ala) to valine (Val) substitution at the 318th amino acid site. Next, HORVU5Hr1G118820 was defined as the candidate gene of MND8 encoding 514 amino acids and containing two multidrug and toxic compound extrusion (MATE) domains. It is highly homologous to maize Bige1 and has a conserved function in the regulation of plant development by controlling the leaf initiation rate. Examination of modern barely varieties showed that Hap-1 was the dominant haplotype and was selected in barley breeding around the world. Collectively, our results indicated that mnd8ynp5 is a novel allele of the HORVU5Hr1G118820 gene that is possibly responsible for the shortened plastochron and many noded dwarf phenotype in barley.

Genomic prediction of threshability in naked barley

AbstractThreshability, defined here as the propensity of grains to lose their hull after harvest, is a key trait in naked barley (Hordeum vulgare L.). While threshability is a defining characteristic of naked grains and has been found to be associated with grain size and shape, its genetic architecture is poorly described. The goals of this study were to identify quantitative trait loci associated with threshability and evaluate their utility as covariates in genomic prediction models. A genome‐wide association study identified two loci on chromosomes 2H and 3H associated with threshability. The locus on chromosome 2H accounted for 9.9% of the phenotypic variance explained (PVE). The locus on chromosomes 3H accounted for 7.8% of the PVE. With effects on threshability of 0.18 and 0.29 for each marker, respectively, these markers could have a limited impact when implemented in marker‐assisted selection. Predictive ability for threshability was 0.842 using a structured genomic best linear unbiased prediction model. Incorporation of the markers with significant associations as covariates in the model did not improve predictive ability. Predictive ability was improved by the use of a multi‐trait model including grain test weight. The high predictive ability for threshability overall indicate that genomic selection would be useful in selection for threshability in naked barley.

Identification of novel and stable genomic regions associated with barley resistance to spot form net blotch disease under different temperature conditions during the reproductive stage

AbstractSpot form net blotch (SFNB) is one of the most important barley diseases in the world; abiotic stresses caused by climate change are also a problem for cultivation of cereals, including barley, on a global level. Identifying stable genomic regions associated with resistance to SFNB in different temperature conditions at the reproductive stage can accelerate the process of producing new cultivars resistant to this disease. In this study, 103 F8 lines, resulting from the cross of cultivars Kavir and Badia, were cultivated in three years on three different dates. After artificial inoculation with Pyrenophora teres f. maculata Gonbad Kavous isolate, the plants were evaluated at the adult stage. The planting dates were chosen so that during early, conventional and delayed planting dates, the reproductive stage of the lines coincided with cold, non‐thermal and heat stress conditions, respectively. A genome‐wide composite interval mapping method was used to identify quantitative trait loci (QTLs) controlling SFNB and estimate the effect of each of them. In the cold, non‐thermal and heat stress conditions at the reproductive stage, three (three major), four (two major) and six (one major) stable resistance QTLs against SFNB were detected, respectively. The stable QTLs of resistance including QRPtma‐2H, QRPtma‐3H and QRPtma‐7H were located on chromosomes 2H, 3H and 7H, respectively. After flanking markers confirm the resistance of QTLs to SFNB, the SCoT7‐C, ISJ17‐B and Bmac0144k markers can be used in the screening resistance of cultivars under non‐thermal and heat stress conditions. Moreover, the Bmac0282b and Ebmatc0016 markers can be used for screening resistance of cultivars under cold stress conditions in marker‐assisted selection projects.

Genome-wide association study of agronomical and root-related traits in spring barley collection grown under field conditions.

The root system is a key component for plant survival and productivity. In particular, under stress conditions, developing plants with a better root architecture can ensure productivity. The objectives of this study were to investigate the phenotypic variation of selected root- and yield-related traits in a diverse panel of spring barley genotypes. By performing a genome-wide association study (GWAS), we identified several associations underlying the variations occurring in root- and yield-related traits in response to natural variations in soil moisture. Here, we report the results of the GWAS based on both individual single-nucleotide polymorphism markers and linkage disequilibrium (LD) blocks of markers for 11 phenotypic traits related to plant morphology, grain quality, and root system in a group of spring barley accessions grown under field conditions. We also evaluated the root structure of these accessions by using a nondestructive method based on electrical capacitance. The results showed the importance of two LD-based blocks on chromosomes 2H and 7H in the expression of root architecture and yield-related traits. Our results revealed the importance of the region on the short arm of chromosome 2H in the expression of root- and yield-related traits. This study emphasized the pleiotropic effect of this region with respect to heading time and other important agronomic traits, including root architecture. Furthermore, this investigation provides new insights into the roles played by root traits in the yield performance of barley plants grown under natural conditions with daily variations in soil moisture content.

The Malting Barley Blues

Malting barley is an economically important crop, with strict quality standards. In some sectors of the industry, there is a bias against malting barley with blue aleurone. The rationale behind this bias is not clear. We therefore investigated the relationships between barley color and malting quality using a panel of fall-planted doubled haploid lines from the Oregon State University barley breeding program. The panel was assessed for malting and aleurone color traits using grain from the 2021 harvest and for aleurone color with grain from the 2022 harvest. The white and blue aleurone groups were found to be different for some malting traits across the entire panel of lines, but this was a result of selection history. When a biparental subset of the panel segregating for aleurone color was considered, differences between the color groups were minimal. A genome wide association study showed that the major QTL contributing to aleurone color (on the long arm of chromosome 4H) was independent of the malt quality QTL. It is concluded that there is no basis for a bias against blue aleurone: identifying new malting barley varieties should be based on their malting performance, not their color.

QTL for induced resistance against leaf rust in barley.

Leaf rust caused by Puccinia hordei is one of the major diseases of barley (Hordeum vulgare L.) leading to yield losses up to 60%. Even though, resistance genes Rph1 to Rph28 are known, most of these are already overcome. In this context, priming may promote enhanced resistance to P. hordei. Several bacterial communities such as the soil bacterium Ensifer (syn. Sinorhizobium) meliloti are reported to induce resistance by priming. During quorum sensing in populations of gram negative bacteria, they produce N-acyl homoserine-lactones (AHL), which induce resistance in plants in a species- and genotype-specific manner. Therefore, the present study aims to detect genotypic differences in the response of barley to AHL, followed by the identification of genomic regions involved in priming efficiency of barley. A diverse set of 198 spring barley accessions was treated with a repaired E. meliloti natural mutant strain expR+ch producing a substantial amount of AHL and a transformed E. meliloti strain carrying the lactonase gene attM from Agrobacterium tumefaciens. For P. hordei resistance the diseased leaf area and the infection type were scored 12 dpi (days post-inoculation), and the corresponding relative infection and priming efficiency were calculated. Results revealed significant effects (p<0.001) of the bacterial treatment indicating a positive effect of priming on resistance to P. hordei. In a genome-wide association study (GWAS), based on the observed phenotypic differences and 493,846 filtered SNPs derived from the Illumina 9k iSelect chip, genotyping by sequencing (GBS), and exome capture data, 11 quantitative trait loci (QTL) were identified with a hot spot on the short arm of the barley chromosome 6H, associated to improved resistance to P. hordei after priming with E. meliloti expR+ch. Genes in these QTL regions represent promising candidates for future research on the mechanisms of plant-microbe interactions.

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials.

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

HvNCX, a prime candidate gene for the novel qualitative locus qS7.1 associated with salinity tolerance in barley

Key MessageA major QTL (qS7.1) for salinity damage score and Na+ exclusion was identified on chromosome 7H from a barley population derived from a cross between a cultivated variety and a wild accession. qS7.1 was fine-mapped to a 2.46 Mb physical interval and HvNCX encoding a sodium/calcium exchanger is most likely the candidate gene.Soil salinity is one of the major abiotic stresses affecting crop yield. Developing salinity-tolerant varieties is critical for minimizing economic penalties caused by salinity and providing solutions for global food security. Many genes/QTL for salt tolerance have been reported in barley, but only a few of them have been cloned. In this study, a total of 163 doubled haploid lines from a cross between a cultivated barley variety Franklin and a wild barley accession TAM407227 were used to map QTL for salinity tolerance. Four significant QTL were identified for salinity damage scores. One (qS2.1) was located on 2H, determining 7.5% of the phenotypic variation. Two (qS5.1 and qS5.2) were located on 5H, determining 5.3–11.7% of the phenotypic variation. The most significant QTL was found on 7H, explaining 27.8% of the phenotypic variation. Two QTL for Na+ content in leaves under salinity stress were detected on chromosomes 1H (qNa1.1) and 7H(qNa7.1). qS7.1 was fine-mapped to a 2.46 Mb physical interval using F4 recombinant inbred lines. This region contains 23 high-confidence genes, with HvNCX which encodes a sodium/calcium exchanger being most likely the candidate gene. HvNCX was highly induced by salinity stress and showed a greater expression level in the sensitive parent. Multiple nucleotide substitutions and deletions/insertions in the promoter sequence of HvNCX were found between the two parents. cDNA sequencing of the HvNCX revealed that the difference between the two parents is conferred by a single Ala77/Pro77 amino acid substitution, which is located on the transmembrane domain. These findings open new prospects for improving salinity tolerance in barley by targeting a previously unexplored trait.

Characterization of a barley (Hordeum vulgare L.) mutant with multiple stem nodes and spikes and dwarf (msnsd) and fine-mapping of its causal gene.

Multiple nodes and dwarf mutants in barley are a valuable resource for identifying genes that control shoot branching, vegetative growth and development. In this study, physiological, microscopic and genetic analysis were conducted to characterize and fine-map the underling gene of a barley mutant with Multiple Stem Nodes and Spikes and Dwarf (msnsd), which was selected from EMS- and 60Co-treated barley cv. Edamai 934. The msnsd mutant had more stem nodes, lower plant height and a shorter plastochron than Edamai 934. Moreover, the mutant had two or more spikes on each tiller. Microscopic analysis showed that the dwarf phenotype of msnsd resulted from reduced cell lengths and cell numbers in the stem. Further physiological analysis showed that msnsd was GA3-deficient, with its plant height increasing after external GA3 application. Genetic analysis revealed that a single recessive nuclear gene, namely, HvMSNSD, controlled the msnsd phenotype. Using a segregating population derived from Harrington and the msnsd mutant, HvMSNSD was fine-mapped on chromosome 5H in a 200 kb interval using bulked segregant analysis (BSA) coupled with RNA-sequencing (BSR-seq), with a C-T substitution in the exon of HvTCP25 co-segregating with the msnsd phenotype. RNA-seq analysis showed that a gene encoding gibberellin 2-oxidase 8, a negative regulator of GA biosynthesis, was upregulated in the msnsd mutant. Several known genes related to inflorescence development that were also upregulated and enriched in the msnsd mutant. Collectively, we propose that HvMSNSD regulates the plastochron and morphology of reproductive organs, likely by coordinating GA homeostasis and changed expression of floral development related genes in barley. This study offers valuable insights into the molecular regulation of barley plant architecture and inflorescence development.