# Identification and characterization of quantitative trait loci (QTLs) associated with waterlogging tolerance in barley (Hordeum vulgare L.)

Li, H 2007 , 'Identification and characterization of quantitative trait loci (QTLs) associated with waterlogging tolerance in barley (Hordeum vulgare L.)', PhD thesis, University of Tasmania.

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## Abstract

Waterlogging is a major environmental constraint severely limiting crop production both in Australia and worldwide. In Australia, most barley cultivars are waterlogging sensitive and increasing their tolerance is an important breeding objective in regions of high rainfall. However, little genetic research and progress has been made on improving barley for waterlogging tolerance, mainly because it is a complex abiotic stress that is affected by many factors such as temperature, plant development stage, nutrient, soil type and topography. The aims of this PhD project were to: (i) investigate the genetic behavior and quantitative inheritance of waterlogging tolerance in barley; (ii) identify and validate quantitative trait loci (QTL) for waterlogging tolerance in barley.
A quantitative genetic analysis of waterlogging was conducted with a 6 X 6 half diallel experiment between three Chinese tolerant cultivars and three susceptible Australian and Japanese cultivars. The six parents and 15 F$$_2$$ from each cross were seeded into two steel tanks (replications), flooded for 10 days and measured for mean yellow leaf percentage. This trait was chosen as other studies have found it to be correlated with waterlogging tolerance. The mean leaf chlorosis of all the F$$_2$$s was similar to that of their mid-parent values. Leaf chlorosis percentages followed an additive model with no significant dominance effect and possessed a high heritability. This experiment demonstrated that selecting in early generations for this trait would be effective.
For the purpose of identification of quantitative trait loci controlling waterlogging tolerance in barley, two linkage maps were constructed, based on doubled haploid populations from crosses between TX9425 (waterlogging tolerant) x Franklin (sensitive), and Yerong (tolerant) x Franklin. The TX9425/Franklin linkage map comprised 412 Diversity Array (DArT) markers, 27 SSR and 81 AFLP markers organized into 8 linkage groups and covering 956 cM. The Yerong/Franklin linkage map was based on 496 DArT and 22 SSR markers assigned to 9 linkage groups and covered 1084.5 cM. The robustness of the DArT markers was confirmed when linkage maps were generated from two sub-sets of progenies in the Y erong/Franklin population, which were genotyped in different batches (arrays). The resuJts indicated that the 496 markers were assigned to exactly the same seven different chromosomes in each of the two experiments. Only minor changes in marker order within chromosomes were found. A relatively large proportion of the molecular markers showed distorted segregation and the possible causes of this are discussed. In order to synthesize the genetic information contained in the two linkage maps produced in this project together with two other maps using DArT markers, a consensus map was constructed which could serve for barley molecular breeding in the future, and as a basis for studies of genome organization and evolution. For example, many more markers showed segregation distortion than expected. Out of the 2975 markers used across all four populations 21.1 %, 10.9%, and 7 .9% exhibited segregation distortion at 5%, 1 %, and 0.5% probability threshold respectively. DArT markers were not more likely to show segregation distortion than other marker types. Of the 63 5 markers showing aberrant segregation in the four populations, 459 markers were located in 16 putative segregation distortion regions (SDR). The SDRs were identified on all seven barley chromosomes, but they were unevenly distributed over the seven chromosomes and their size varied from 4 to 46 cM. Ten of the SDRs were found in at least two populations and several at a consistent map location over the four populations. Further studies are needed to determine the molecular basis of segregation distortion.
In order to detect QTL for waterlogging tolerance in barley, the two mapping populations were tested for germination (six replicates of fifty seeds each, submerged in 50 ml of water for six days, then moved to incubators for germination), leaf chlorosis, biomass reduction and survival (four replicates (tanks), five plants from each DH and parental lines sown in pots, placed in tanks, three of which were flooded and one used as a control). QTL analysis found a total of 6 distinct QTLs for the four traits in the Franklin/TX9425 population and 6 QTLs in the Franklin/Y erong population. QTL controlling leaf chlorosis were quite similar in their location between the two populations, the most important QTL found being in the same region of chromosome 3H in each population. One QTL controlling plant survival rate was located on chromosome 2H in both populations. A QTL for biomass reduction was identified in each population to chromosome 4H. However, it may not be the same QTL because they mapped to slightly different regions of that chromosome in each population. A QTL for seed germination was located on chromosome lH in the Franklin/TX9425 population. However, this QTL was different from the QTL controlling leaf chlorosis, which mapped to a different region of the same chromosome. In this study strong QTLs were identified, which could be cross-validated in different mapping population for traits correlated with waterlogging tolerance in barley. Thus there is good scope for using marker assisted selection in breeding for waterlogging tolerance in barley. However, these QTL will need to be further validated through field experiments and yield measurements under waterlogging conditions.

Item Type: Thesis - PhD Li, H Barley Copyright 2007 the author View statistics for this item