Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality

<p>Abstract</p> <p>Background</p> <p>The increasingly narrow genetic background characteristic of modern crop germplasm presents a challenge for the breeding of cultivars that require adaptation to the anticipated change in climate. Thus, high priority research aims at the identification of relevant allelic variation present both in the crop itself as well as in its progenitors. This study is based on the characterization of genetic variation in barley, with a view to enhancing its response to terminal drought stress.</p> <p>Results</p> <p>The expression patterns of drought regulated genes were monitored during plant ontogeny, mapped and the location of these genes was incorporated into a comprehensive barley SNP linkage map. Haplotypes within a set of 17 starch biosynthesis/degradation genes were defined, and a particularly high level of haplotype variation was uncovered in the genes encoding sucrose synthase (types I and II) and starch synthase. The ability of a panel of 50 barley accessions to maintain grain starch content under terminal drought conditions was explored.</p> <p>Conclusion</p> <p>The linkage/expression map is an informative resource in the context of characterizing the response of barley to drought stress. The high level of haplotype variation among starch biosynthesis/degradation genes in the progenitors of cultivated barley shows that domestication and breeding have greatly eroded their allelic diversity in current elite cultivars. Prospective association analysis based on core drought-regulated genes may simplify the process of identifying favourable alleles, and help to understand the genetic basis of the response to terminal drought.</p

Understanding terminal drought tolerance in barley using AB-QTL analysis and an integrated omics approach

Trockenheit ist eine der Hauptbeschränkungen der Produktivität bei Gerste und beeinträchtigt Samenertrag und –qualität. Das Hauptziel der vorliegenden Arbeit war die Mechanismen der terminalen Trockentoleranz (in der letzten Phase der Pflanzenentwicklung) unter Verwendung zweier komplementärer Ansätze zu verstehen. Zunächst wurde ein AB-QTL-Ansatz (Advanced Backcross-Quantitative Trait Locus) angewendet, um eingebrachte Regionen einer Wildgerste zu identifizieren, die die terminale Trockentoleranz beeinflussen. Dazu wurde eine Population von Introgressionslinien (BC3-DH) verwendet, die aus der Kreuzung zwischen dem Gerstenkultivar Brenda und einer Gersten-Wildform (Hs 584) entwickelt wurden. Zweitens wurde eine integrierter omics-Ansatz (Transkriptom und Metabolite) verwendet, um die Wichtigkeit von „Stay-green-“ / Seneszenzmechanismen in Gerste unter terminaler Trockenheit zu verstehen. In diesem Ansatz wurden Elite-Züchtungslinien untersucht. Trockenstress wurde entweder durch Behandlung mit Kaliumiodid oder durch Bewässerungsstopp 10 Tage nach der Blüte erreicht. Die signifikante Beteiligung verschiedener QTLs für Ertrag und Samenqualität durch Hs584 illustrieren das Potenzial der Wildgerste in der Züchtung, um verbesserte Sorten bei optimalen sowie Trockenstress-Bedingungen zu erhalten. Bezüglich des zweiten Ansatzes bekräftigt diese Arbeit, dass die seneszenz-induzierte Remobilisierung von Stängelreservestoffen einen wichtigen Teil während der Samenfüllung bei Trockenstress darstellt. Der Genotyp LP104, der durch einen seneszierenden Phäntotyp charakterisiert ist, zeigte eine bessere Leistung in Bezug auf Samenertrag und –qualität bei Trockenstress verglichen mit dem „stay-green“ Gentotyp LP106. Trotz eines höheren Gehaltes an wasserlöslichen Zuckern im Stängel deutet die schlechtere Leistung bezüglich der Stängelremobilisierung des „stay-green“ Gentotyps darauf hin, dass das Stängelgewicht/Anteil der wasserlöslichen Kohlenhydrate zur Blüte allein nicht als sekundärer Parameter für das Screening nach Trockentoleranz in Gerste herangezogen werden kann. Die schlechtere Leistung eines weiteren seneszierenden Genotyps, LP110, verglichen mit LP104 hinsichtlich der Stickstoffremobilisierung deutet zudem auf die Tatsache hin, dass Seneszenz allein nicht ausreichend für die Remobilisierung von gespeicherten Reserven ist. Dieser Aspekt muss noch detaillierter untersucht werden.Terminal drought is one of the major constraints for barley production that affects both seed yield and quality. The major objective of this investigation was to understand the mechanism of terminal drought tolerance for seed yield and quality using two complementary approaches. Firstly, an advanced backcross quantitative trait locus (QTL) analysis was carried out to identify exotic regions influencing terminal drought tolerance using a BC3-DH population developed between the cultivated parent Brenda and the wild accession, HS584. Secondly, an integrated omics (transcripts and metabolites) together with various physiological parameters were used o characterize the significance of staygreen/senescence mechanisms under terminal drought using contrasting elite breeding lines exhibiting staygreen and senescence phenotypes. Terminal drought was imposed by either spraying with potassium iodide or withholding water at 10 days after flowering. Significant contribution of various QTL for yield and seed quality parameters by HS584 indicated that wild barley is a potential source of terminal drought tolerance in various breeding programmes. With respect to second approach, our study reinforces that senescence induced remobilization of stem reserves is an important component of seed filling under terminal drought. LP104, characterized by senescence phenotype performed better compared to staygreen in terms of both seed yield and quality under terminal drought. In spite of higher stem water soluble sugars (WSC) in the staygreen genotype, its poor performance with respect to stem remobilization compared to senescing (LP104) indicates that stem weight/WSC at anthesis alone cannot be considered as a secondary parameter to screen for terminal drought tolerance in barley. The poor performance of one of the senescing genotypes, LP110 compared to LP104 with respect to leaf nitrogen remobilization also hints to the fact that senescence alone may not be sufficient for remobilization of stored reserves, which is to be explored in great detail.von Rajesh Kallada

Natural Variation in 9-Cis-Epoxycartenoid Dioxygenase 3 and ABA Accumulation

The stress hormone abscisic acid (ABA) is critical for drought resistance; however, mechanisms controlling ABA levels are unclear. At low water potential, ABA accumulation in the Arabidopsis (Arabidopsis thaliana) accession Shahdara (Sha) was less than that in Landsberg erecta (Ler) or Columbia. Analysis of a Ler 3 Sha recombinant inbred line population revealed a single major-effect quantitative trait locus for ABA accumulation, which included 9-cis-epoxycarotenoid dioxygenase3 (NCED3) as a candidate gene. NCED3 encodes a rate-limiting enzyme for stress-induced ABA synthesis. Complementation experiments indicated that Sha has a reduced-function NCED3 allele. Compared with Ler, Sha did not have reduced NCED3 gene expression or protein level but did have four amino acid substitutions within NCED3. Sha differed from Ler in the apparent molecular mass of NCED3, indicative of altered NCED3 proteolytic processing in the chloroplast. Site-directed mutagenesis demonstrated that substitution at amino acid 271 was critical for the altered NCED3 molecular mass pattern, while the other Sha NCED3 polymorphisms were also involved in the reduced ABA accumulation. Sha did not have a reduced level of thylakoidbound NCED3 but did differ from Ler in the apparent molecular mass of stromal NCED3. As Sha was not impaired in known factors critical for NCED3 function in ABA synthesis (expression, chloroplast import, and thylakoid binding), the differences between Ler and Sha NCED3 may affect NCED3 activity or other factors influencing NCED3 function. These results identify functionally important sites on NCED3 and indicate a complex pattern of NCED3 posttranslational regulation in the chloroplast