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Exploring genetics associated with phenology and grain quality in barley (Hordeum vulgare L.)


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Ahmed, ID ORCID: 0000-0001-5597-7087 2019 , 'Exploring genetics associated with phenology and grain quality in barley (Hordeum vulgare L.)', PhD thesis, University of Tasmania.

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Barley (Hordeum vulgare) is ranked fourth among the cereals in the world today and second in size to wheat in Australia. It is an important crop mainly used for malting and feed. Climatic extremes and variability often limit potential barley production. Frost and drought, for example, may result in up to 80% and total grain yield loss, respectively. The most vulnerable growth period of an actively growing cereal crop is the reproductive phase, including the spikelet initiation, heading and grain filling stages. Heading date is one of the most important traits for improving barley stress tolerance to drought, heat, waterlogging and frost. Well timed duration and date of ear emergence and grain filling can improve yield in environments prone to frost, water deficits and/or heatwaves. Therefore, identification of the genetic factors controlling these traits and mechanisms of regulation including their interactions will facilitate breeding efforts to adapt genotypes for specific environment given the challenges of climate variability facing barley production.
Although ear emergence in barley is a quantitative trait that is influenced by vernalisation, growing‐degree‐days (GDD) and daylength, the trait is primarily controlled by three groups of genes. Genes with major effects include photoperiod, Ppd (Ppd‐H1 and Ppd‐H2) on chromosomes 2H and 1H respectively, and vernalisation, Vrn (Vrn‐H1, Vrn‐H2, Vrn‐H3 and Vrn‐H4), on chromosomes 5H, 4H, 7H and 5H, respectively. Genes with minor effects include earliness per se Eps and HvPHYC. The Ppd, Vrn and Eps genes have been deployed in many breeding programs so that ear emergence and grain‐filling periods may occur within favourable conditions, and with consequent stress avoidance thereby optimising biomass production and yield potential.
Wild barley genotypes show a diversity in various traits from cultivated barley. Using a doubled haploid barley population sown in three seasons differing in daylength and temperature, quantitative trait loci controlling heading date from different populations and growing seasons were investigated. Of the two parents, SYR01 is a Syrian wild barley and Gairdner is an Australian malting barley. A total of 173 DH lines were genotyped with DArT and SNP makers. The heading dates were phenotyped using three sowing dates (winter and spring and summer) to test the photoperiod/temperature responses of different QTL. DH lines showed a transgressive segregation; DH lines were significantly different from the parents in heading date. Eight QTL were identified for heading date from different sowing dates under field conditions, accounting for 7‐47% of the phenotypic variation. The locations of most QTL in this study coincide with the positions of the earlier reported genes, including Ppd‐H1 on 2H, Eps genes on 3H, Vrn‐H2 on 4H. Others include Vrn‐H1, Eps on 5H, Eps.6S on 6H and Vrn‐H3 on 7H. Vrn genes were only identified in spring sowing trials. One QTL (Qhd‐sg‐2H.1w) on 2H was located in a different position from Ppd‐H1 and (Qhd‐sg‐5HL.3s) on 5H; these QTL requires further investigation to confirm if they are new genes for heading date. This study confirmed the results of previously reported genes, most of which have been conducted in greenhouse. Our study demonstrates the important role of genetic interaction that regulates heading date under natural production environments in barley. Finally, this study showed that the QTL within region of 122.5 and 126.1 cM influencing early maturity in the NILs consist of an Eps gene different from Vrn‐H1 and HvPHYC and has pleiotropic effects on agronomic traits like spike length and number of spikelets per spike. Cultivation of the early maturing genotype of the NILs is more suitable in drought prone short seasoned environment while the late genotype is more adapted to longer season conditions indicating that process‐based models can effectively complement breeding efforts in determining the performance of new genotypes in new environments under diverse management conditions. The study involving DH lines of SYR01 x Gairdner under field conditions validates the previously identified QTL, which were mostly detected under controlled environment. with two new QTL (Qhd‐sg‐ 2H.1w) on 2H and(Qhd‐sg‐5HL.3s) located in a different position on 2H and 5H respectively further investigation is required to confirm if they are new genes for heading date with the anticipation of delivering the closely linked molecular markers with these genes to breeders and farmers.
In our previous studies, a new allele for early flowering was identified from the cross between an Australian malting barley cultivar (Franklin) and a Chinese landrace (TX9425). Four sets of near isogenic lines (NILs, Eps5H‐116, Eps5H‐317‐1, Eps5H‐317‐2 and Eps5H‐322) were located on chromosome 5H at the interval of 122.0‐129.0 cM. Further experiments were conducted to investigate how this gene was regulated by photoperiod using the NILs with three sowing dates from autumn to summer. The NILs carrying the earliness allele were significantly earlier than the late genotype at all sowing dates. This gene was different from previously reported vernalisation genes that are located at a similar position, as no vernalisation was required for the NILs. The difference between this gene and Eam5 (HvPHYC) locus which also located between two co‐segregated markers (3398516S5, 122.5 cM, and 4014046D5, 126.1 cM), is that with the existence of Ppd‐H1 (Eam1), Eam5 has no effect on ear emergence under long days while the gene from TX9425 reduced the time to ear emergence. The locus showed no pleiotropic effects on grain pasting properties and agronomic traits except for spike length and number of spikelets per spike, and thus can be effectively used in breeding programs for heading date. The array of early heading dates caused by interactions between Eam5 gene from Eps5H‐317‐1‐E and other maturity genes provides an opportunity to fine tune heading dates with environment types, which can be critical factor in barley breeding.
Two of the four NILs (Eps‐317‐1‐E, and Eps‐317‐1‐L) were selected to be used in field experiments which were conducted in Tasmania, Australia, using three sowing dates per year during 2015, 2016 and 2017 to parameterise and test the barley module of the APSIM model (APSIM‐Barley). Parental lines Franklin and TX9425 were also parameterised in the model. A genotype by environment by management (GxExM) analysis was then conducted using ten sites across the Australian wheat‐belt, with a range of sowing dates, fertiliser rates and planting densities. The early genotype (Eps‐317‐1‐E) performed better in environments prone to terminal drought and heat stress effects. This was due to earlier flowering and a propensity for greater transpiration‐use efficiency from growth stage (GS) 50 to 87. The late NIL (Eps‐317‐1‐L) generally produced higher yield in long‐season environments with high rainfall and cool terminal temperatures. Performance of all genotypes was generally better for May sowings, wherein yields of the two NILs were highest. This better yield performance of the NILs was due to heterosis resulting to more biomass and consequently greater harvest index. Overall, our study showed that Eps‐317‐1‐E is more adapted to regions prone to drought and heat stress, while Eps‐317‐1‐L is more suited to regions with longer growing seasons. This study demonstrates how process‐based models can be used in concert with breeding experiments, providing farmers and breeders with opportunities to examine how new genotypes will perform in new environments under diverse management conditions.

Item Type: Thesis - PhD
Authors/Creators:Ahmed, ID
Keywords: Barley, quantitative trait loci, heading-date, Environment, management, yield, quality
DOI / ID Number: 10.25959/100.00031405
Copyright Information:

Copyright 2018 the author

Additional Information:

Chapter 2 appears to be the equivalent of a post-print version of a book chapter published as: Ibrahim, A., Harrison, M., Meinke, H., Zhou, M., 2016. Barley phenology: physiological and molecular mechanisms for heading date and modelling of genotype‐environment‐management interactions, in, Planbt growth, Rigobelo (ed.), Intech Open. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution 3.0 Unported (CC BY 3.0) License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Chapter 3 appears to be the equivalent of a post-print version of an article published as: Ibrahim, A., Harrison, M., Meinke, H., Fan, Y., Johnson, P., Zhou, M. (2018a). A regulator of early flowering in barley (Hordeum vulgare L.). PLoS ONE 13(7), e0200722. Copyright: © 2018 Ibrahim et al. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License, ( which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Chapter 4 appears to be the equivalent of a pre-print version of an article published as: Ibrahim, A., Harrison, M. T., Meinke, H., Zhou, M., 2019. Examining the yield potential of barley near-isogenic lines using a genotype by environment by management analysis, European journal of agronomy, 105, 41-51

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