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Mapping QTL for salinity tolerance and its related physiological traits in barley (Hordeum vulgare L.)


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Fan, Y (2016) Mapping QTL for salinity tolerance and its related physiological traits in barley (Hordeum vulgare L.). PhD thesis, University of Tasmania.

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Soil salinity is one of the major abiotic stresses which severely affect crop yield and restrict the utilization of agricultural land. Breeding salt tolerant crops has become one of the top priorities, as salinity is causing global food issues due to the large arable and saline area which are not suitable for cropping. Salinity stress is considered to be composed of two phases at the whole-plant level: a rapid osmotic stress which reduces shoot growth, and slower ionic stress which accelerates senescence of older leaves due to elevated leaf Na+ content. Osmotic stress affects plant growth by reducing cell expansion and elongation rates, which leads to smaller and thicker leaves and down-regulated photosynthesis by reducing stomatal aperture. Plants employ numerous mechanisms to adapt to saline conditions such as Na+ exclusion from uptake, control of xylem Na+ loading and/or its retrieval from the shoot, efficient vacuolar Na+ sequestration, efficient osmotic adjustment, and ROS detoxification. Since many traits underlying adaption to stress are quantitative and controlled by multiple genetic pathways, a wide variety of genes are implicated in salinity tolerance.
Molecular marker assisted selection (MAS) has been successfully used in barley breeding programs, particularly for traits which are easily affected by environments. However, less progress has been made in salt tolerance due to the lack of efficient QTL that can be used MAS. The objective of this study were (i) to detect QTL controlling salinity tolerance and some physiological traits using different barley populations; (ii) to investigate the contribution of different physiological traits to plant overall salinity tolerance; (iii) to study the relationships between QTL for agronomic and physiological traits and those for plant drought and salinity tolerance using QTL mapping; (iv) to fine map a QTL for salinity tolerance which has been identified in our previous work.
ROS detoxification is one of the salinity tolerance mechanisms in plants, which includes enzymatic and non- enzymatic scavenging. To investigate the role of major antioxidant (AO) enzymes in plant salinity tolerance and whether it is suitable for using as selection criteria of salinity tolerance, two barley varieties with contrast salinity tolerance (TX9425 & Naso Nijo) were firstly used to evaluate the activity of major AO enzymes in different leaves and at different times after salt treatment. Our results showed that AO enzyme activities had strong tissue- and time-specificity. A further study was conducted using six barley varieties contrasting in salinity tolerance (TX9425, YYXT, CM72, Naso Nijo, Franklin and Gairdner). AO enzyme activities and proline contents were measured in the third leaves of seedlings after plants were treated with 240 mM NaCl for 10 days. No significant correlation was revealed between leaf AO activity and either plant grain yield or plant survival rate under salt stress. Although salinity induces changes in leaf AO enzyme activities, the change cannot be used as biochemical indicator in breeding for salinity tolerance.
A double haploid (DH) population from the cross of TX9425 (a Chinese landrace variety with both salinity and drought tolerance) and Franklin (sensitive to both salinity and drought) was used to identify QTL for salinity and drought tolerance. One QTL for salinity tolerance on 7H based on plant survival under salt stress and two QTL for drought tolerance on 2H and 5H using leaf wilting under drought stress conditions were identified from this population. The QTL for proline accumulation under both salinity and drought stresses were located on different positions to those for drought and salinity tolerance, indicating no relationship with plant tolerance to either of these stresses. It was also shown that proline accumulation under stresses was merely a symptom of plant damage thus not to be a useful selection criterion for either drought or salinity tolerance.
Stomata regulate photosynthesis and transpiration, which are critical for plant responses to abiotic stresses such as salinity. To understand the genetic basis controlling salinity tolerance and stomatal parameters, a DH population from the cross of CM72 and Gairdner was used to detect QTL underlying these traits. Total of 11 significant QTL (LOD > 3.0) and 11 tendency QTL (2.5 < LOD < 3.0) were investigated distributing on all different chromosomes except for 5H. Co-localization of QTL for biomass with that for intercellular CO2 concentration, transpiration rate and stomatal conductance was found under control condition. A QTL for biomass also co-located with one for transpiration rate under salinity stress. The QTL for salinity tolerance also co-localised with QTL for grain yield on chromosome 3H. The lack of major QTL for gas exchange and stomatal traits under control and saline conditions indicates a complex relationship between salinity and leaf gas exchange and the fact that these complex quantitative traits are under the control of multiple genes.
A wide range of barley accessions were used to detect genetic variations through genome wide association study (GWAS). The 206 barley accessions collected worldwide were genotyped with 408 Diversity Arrays Technology (DArT) markers and evaluated for salinity stress tolerance using plant damage scores under salinity stress – a reliable method developed in our previous work. GWAS for salinity tolerance had been conducted through a general linkage model (GLM) and a mixed linkage model (MLM) based on population structure and kinship. A total of 24 significant marker-trait associations were identified. A QTL on 4H with the nearest marker of bpb-9668 was consistently detected in all different methods. This QTL has not been reported before and is worth to be further confirmed with bi-parental population.
A major QTL for salinity tolerance was identified in the DH population from the cross between TX9425 and Naso Nijo in our previous study. This QTL explained more than 45% of the phenotypic variation. Further fine mapping has been conducted to this population. A new marker was identified to be more closely linked to this gene, determining more than 70% of the phenotypic variation. Near isogenic lines have been developed for further fine mapping, physiological studies and the identification of gene(s).
In conclusion, several QTL were identified for salinity tolerance and its related physiological traits, including Na+ content, proline content, stomata pore area, leaf temperature and transpiration rate. The QTL for salinity tolerance on 3H from the cross of CM72 and Gairdner was located at the same position as that for grain yield under salinity stress. Most of the QTL for physiological traits were located at different positions to those for salinity tolerance. One new QTL for salinity tolerance was detected through genome wide association studies and this QTL will be further confirmed by bi-parental populations. We have also fine mapped a major QTL that was reported earlier to less than 2 cM. Near isogenic lines were constructed for further fine mapping and studies on gene expression. ROS antioxidants were found to be affected by numerous factors such as leaf age, salt concentration and treatment time, thus can’t be used as indirect selection criteria for salinity tolerance.

Item Type: Thesis (PhD)
Keywords: Salinity tolerance, Quantitative trait locus, mapping, Barley
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Copyright 2016 the Author

Additional Information:

Chapter 2 has been published as: Fan, Y., Bose, J., Zhou, M., Shabala, S. 2015. ROS production, scavenging and signalling under salinity stress. In: Wani, S. H., Hossain, M. A., eds. Managing salinity tolerance in plants: molecular and genomic perspectives, CRC Press, Taylor & Francis Group

Chapter 3 appears to be the equivalent of the peer reviewed version of the following article: Fan, Y., Zhu, M., Shabala, S., Li, C. D., Johnson, P., Zhou, M. X., 2014. Antioxidant activity in salt-stressed barley leaves: evaluating time- and age-dependence and suitability for the use as a biochemical marker in breeding programs, Journal of agronomy and crop science, 200(4), 261-272, which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

Chapter 4 appears to be the equivalent of a post-print version of an article published as: Fan, Y., Shabala, S., Ma, Y., Xu, R., Zhou, M., 2015. Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits, BMC genomics, 16(1), 43, 1-11

Chapter 5 appears to be the equivalent of a post-print version of an article published as: Lui, X., Yan, F., Mak, M. et al., 2017. QTLs for stomatal and photosynthetic traits related to salinity tolerance in barley, BMC genomics, 18(9), 1-13

Chapter 6 appears to be the equivalent of a post-print version of an article published as: Fan, Y., Zhou, G. F., Shabala, S., Chen, Z. H., Cai, S. G., Li, C. D., Zhou, M. X., 2016. Genome-wide association study reveals a new QTL for salinity tolerance in barley (Hordeum vulgare L.), Frontiers in plant science, 7: 946, 1-10. This document is protected by copyright and was first published by Frontiers. All rights reserved. It is reproduced with permission.

Date Deposited: 10 Apr 2017 22:48
Last Modified: 26 Jul 2017 02:27
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