Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition

Identifying developmental QTL alleles with favorable effect on grain yield components under late-terminal drought in spring barley MAGIC population

Barley is the fourth most cultivated cereal worldwide, and drought is a major cause of its yield loss by negatively affecting its development. Hence, better understanding developmental mechanisms that control complex polygenic yield-related traits under drought is essential to uncover favorable yield regulators. This study evaluated seven above-ground yield-related traits under well-watered (WW) and late-terminal drought (TD) treatment using 534 spring barley multiparent advanced generation intercross double haploid (DH) lines. The analysis of quantitative trait loci (QTL) for WW, TD, marker by treatment interaction, and drought stress tolerance identified 69, 64, 25, and 25 loci, respectively, for seven traits from which 15 loci were common for at least three traits and 17 were shared by TD and drought stress tolerance. Evaluation of allelic effects for a QTL revealed varying effect of parental alleles. Results showed prominent QTL located on major flowering time gene Ppd-H1 with favorable effects for grain weight under TD when flowering time was not significantly affected, suggesting that this gene might be linked with increasing grain weight by ways other than timing of flowering under late-terminal drought stress. Furthermore, a desirable novel QTL allele was identified on chromosome 5H for grain number under TD nearby sucrose transporter gene HvSUT2. The findings indicated that spring barley multiparent advanced generation intercross population can provide insights to improve yield under complex condition of drought.

Identification of QTL underlying the main stem related traits in a doubled haploid barley population

Lodging reduces grain yield in cereal crops. The height, diameter and strength of stem are crucial for lodging resistance, grain yield, and photosynthate transport in barley. Understanding the genetic basis of stem benefits barley breeding. Here, we evaluated 13 stem related traits after 28 days of heading in a barley DH population in two consecutive years. Significant phenotypic correlations between lodging index (LI) and other stem traits were observed. Three mapping methods using the experimental data and the BLUP data, detected 27 stable and major QTLs, and 22 QTL clustered regions. Many QTLs were consistent with previously reported traits for grain filling rate, internodes, panicle and lodging resistance. Further, candidate genes were predicted for stable and major QTLs and were associated with plant development and adverse stress in the transition from vegetative stage to reproductive stage. This study provided potential genetic basis and new information for exploring barley stem morphology, and laid a foundation for map-based cloning and further fine mapping of these QTLs.

QTLs Controlling Physiological and Morphological Traits of Barley (Hordeum vulgare L.) Seedlings under Salinity, Drought, and Normal Conditions

To identify the genomic regions for the physiological and morphological traits of barley genotypes under normal salinity and drought, a set of 103 recombinant inbred line (RIL) populations, developed between Badia and Kavir crosses, was evaluated under phytotron conditions in a completely randomized design in 2019. Linkage maps were prepared using 152 SSR markers, 72 ISSR, 7 IRAP, 29 CAAT, 27 SCoT, and 15 iPBS alleles. The markers were assigned to seven barley chromosomes and covered 999.29 centimorgans (cM) of the barley genome. In addition, composite interval mapping showed 8, 9, and 26 quantitative trait loci (QTLs) under normal, drought, and salinity stress conditions, respectively. Our results indicate the importance of chromosomes 1, 4, 5, and 7 in salinity stress. These regions were involved in genes controlling stomata length (LR), leaf number (LN), leaf weight (LW), and genetic score (SCR). Three major stable pleiotropic QTLs (i.e., qSCS-1, qRLS-1, and qLNN-1) were associated with SCR, root length (RL), and root number (RN) in both treatments (i.e., normal and salinity), and two major stable pleiotropic QTLs (i.e., qSNN-3 and qLWS-3) associated with the stomata number (SN) and LW appeared to be promising for marker-assisted selection (MAS). Two major-effect QTLs (i.e., SCot8-B-CAAT5-D and HVM54-Bmag0571) on chromosomes 1 and 2 were characterized for their positive allele effect, which can be used to develop barley varieties concerning drought conditions. The new alleles (i.e., qLWS-4a, qSLS-4, qLNS-7b, qSCS-7, and qLNS-7a) identified in this study are useful in pyramiding elite alleles for molecular breeding and marker assisted selection for improving salinity tolerance in barley.

Au-courant and novel technologies for efficient doubled haploid development in barley (Hordeum vulgare L.)

Bounteous modern and innovative biotechnological tools have resulted in progressive development in the barley breeding program. Doubled haploids developed (homozygous lines) in a single generation is significant. Since the first discovery of haploid plants in 1920 and, in particular, after discovering in vitro androgenesis in 1964 by Guha and Maheshwari, the doubled haploidy techniques have been progressively developed and constantly improved. It has shortened the cultivar development time and has been extensively used in: genetic studies, gene mapping, marker/trait association, and QTL studies. In barley, the haploid occurrence developed gradually from being a sporadic and random process (spontaneous) to haploid development by in vivo method of modified pollination or by in vitro culture of immature male or female gametophytes. Although significant improvement in DH induction protocols has been made, challenges still exist for improvement in areas such as: low efficiency, albinism, genotypic specificity etc. Here, the paper focuses on: haploidization via different in vitro, in vivo techniques, the recent advances technologies like centromere-mediated haploidization, hap induction gene, and Doubled haploid CRISPR. The au-courant work of different researchers in barley using these technologies is reviewed. Studies on different factors affecting haploid induction and work on genome doubling of barley haploids to produce DH lines via spontaneous and induced technologies has also been highlighted.

QTL Mapping and Phenotypic Variation for Seedling Vigour Traits in Barley (Hordeum vulgare L.)

Seed vigour is considered a critical stage for barley production, and cultivars with early seedling vigour (ESV) facilitate rapid canopy formation. In this study, QTLs for 12 ESV-related traits were mapped using 185 RILs derived from a Xena x H94061120 evaluated across six independent environments. DArT markers were used to develop a genetic map (1075.1 cM; centimorgans) with an average adjacent-marker distance of 3.28 cM. In total, 46 significant QTLs for ESV-related traits were detected. Fourteen QTLs for biomass yield were found on all chromosomes, two of them co-localized with QTLs on 1H for grain yield. The related traits: length of the first and second leaves and dry weight of the second leaf, biomass yield and grain yield, had high heritability (>30%). Meanwhile, a significant correlation was observed between grain yield and biomass yield, which provided a clear image of these traits in the selection process. Our results demonstrate that a pleiotropic QTL related to the specific leaf area of the second leaf, biomass yield, and grain yield was linked to the DArT markers bPb-9280 and bPb-9108 on 1H, which could be used to significantly improve seed vigour by marker-assisted selection and facilitate future map-based cloning efforts.

Mapping dynamic QTL dissects the genetic architecture of grain size and grain filling rate at different grain-filling stages in barley

Grain filling is an important growth process in formation of yield and quality for barley final yield determination. To explore the grain development behavior during grain filling period in barley, a high-density genetic map with 1962 markers deriving from a doubled haploid (DH) population of 122 lines was used to identify dynamic quantitative trait locus (QTL) for grain filling rate (GFR) and five grain size traits: grain area (GA), grain perimeter (GP), grain length (GL), grain width (GW) and grain diameter (GD). Unconditional QTL mapping is to detect the cumulative effect of genetic factors on a phenotype from development to a certain stage. Conditional QTL mapping is to detect a net effect of genetic factors on the phenotype at adjacent time intervals. Using unconditional, conditional and covariate QTL mapping methods, we successfully detected 34 major consensus QTLs. Moreover, certain candidate genes related to grain size, plant height, yield, and starch synthesis were identified in six QTL clusters, and individual gene was specifically expressed in different grain filling stages. These findings provide useful information for understanding the genetic basis of the grain filling dynamic process and will be useful for molecular marker-assisted selection in barley breeding.

Dissecting the Genetic Basis of Grain Size and Weight in Barley (Hordeum vulgare L.) by QTL and Comparative Genetic Analyses

Grain size and weight are crucial components of barley yield and quality and are the target characteristics of domestication and modern breeding. Despite this, little is known about the genetic and molecular mechanisms of grain size and weight in barley. Here, we evaluated nine traits determining grain size and weight, including thousand grain weight (Tgw), grain length (Gl), grain width (Gw), grain length-width ratio (Lwr), grain area (Ga), grain perimeter (Gp), grain diameter (Gd), grain roundness (Gr), and factor form density (Ffd), in a double haploid (DH) population for three consecutive years. Using five mapping methods, we successfully identified 60 reliable QTLs and 27 hotspot regions that distributed on all chromosomes except 6H which controls the nine traits of grain size and weight. Moreover, we also identified 164 barley orthologs of 112 grain size/weight genes from rice, maize, wheat and 38 barley genes that affect grain yield. A total of 45 barley genes or orthologs were identified as potential candidate genes for barley grain size and weight, including 12, 20, 9, and 4 genes or orthologs for barley, rice, maize, and wheat, respectively. Importantly, 20 of them were located in the 14 QTL hotspot regions on chromosome 1H, 2H, 3H, 5H, and 7H, which controls barley grain size and weight. These results indicated that grain size/weight genes of other cereal species might have the same or similar functions in barley. Our findings provide new insights into the understanding of the genetic basis of grain size and weight in barley, and new information to facilitate high-yield breeding in barley. The function of these potential candidate genes identified in this study are worth exploring and studying in detail.