Abiotic Stress and Agronomic Traits
Root Biomass and Drought Tolerance
References
1. Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice. Nguyen TTT, Klueva N, Chamareck V, Aarti A, Magpantay G, Millena ACM, Pathan MS, Nguyen HT. In: Molecular and General Genomics, 2004, 272: 35-46.
We have developed 85 new markers (50 RFLPs, 5 SSRs, 12 DD cDNAs, 9 ESTs, 8 HSP- encoding cDNAs and one BSA-derived AFLP marker) for saturation mapping of QTL regions for drought tolerance in rice, in our efforts to identify putative candidate genes. Thirteen of the markers were localized in the close vicinity of the targeted QTL regions. Fifteen of the additional markers mapped, respectively, inside one QTL region controlling osmotic adjustment on chromosome 3 ( oa3.1) and 14 regions that affect root traits on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 10 and 12. Differential display was used to identify more putative candidate genes and to saturate the QTL regions of the genetic map. Eleven of the isolated cDNA clones were found to be derived from drought-inducible genes. Two of them were unique and did not match any genes in the GenBank, while nine were highly similar to cDNAs encoding known proteins, including a DnaJ-related protein, a zinc-finger protein, a protease inhibitor, a glutathione-S-transferase, a DNA recombinase, and a protease. Twelve new cDNA fragments were mapped onto the genetic linkage map; seven of these mapped inside, or in close proximity to, the targeted QTL regions determining root thickness and osmotic adjustment capacity. The gene I12A1, which codes for a UDP-glucose 4-epimerase homolog, was identified as a putative target gene within the prt7.1/brt7.1 QTL region, as it is involved in the cell wall biogenesis pathway and hence may be implicated in modulating the ability of rice roots to penetrate further into the substratum when exposed to drought conditions. RNAs encoding elongation factor 1b, a DnaJ-related protein, and a homolog of wheat zinc-finger protein were more prominently induced in the leaves of IR62266 (the lowland rice parent of the mapping materials used) than in those of CT9993 (the upland rice parent) under drought conditions. Homologs of 18S ribosomal RNA, and mRNAs for a multiple stress induced zinc-finger protein, a protease inhibitor, and a glutathione-S-transferase were expressed at significantly higher levels in CT9993 than in IR62266. Thus several genes involved in the regulation of DNA structure and mRNA translation were found to be drought-regulated, and may be implicated in drought resistance.
2. A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring x SQ1 and its use to compare QTLs for grain yield across a range of environments. Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, Chinoy C, Steele N, Pljevljakusic D, Waterman E, Weyen J, Schondelmaier J, Habash DZ, Farmer P, Saker L, Clarkson DT, Abugalieva A, Yessimbekova M, Turuspekov Y, Abugalieva S, Tuberosa R, Sanguineti M-C, Hollington PA, Aragués R, Royo A, Dodig D. In: Theoretical and Applied Genetics, 2005, 110:865-880.
A population of 96 doubled haploid lines (DHLs) was prepared from F1 plants of the hexaploid wheat cross Chinese Spring x SQ1 (a high abscisic acid-expressing breeding line) and was mapped with 567 RFLP, AFLP, SSR, morphological and biochemical markers covering all 21 chromosomes, with a total map length of 3,522 cM. Although the map lengths for each genome were very similar, the D genome had only half the markers of the other two genomes. The map was used to identify quantitative trait loci (QTLs) for yield and yield components from a combination of 24 site · treatment · year combinations, including nutrient stress, drought stress and salt stress treatments. Although yield QTLs were widely distributed around the genome, 17 clusters of yield QTLs from five or more trials were identified: two on group 1 chromosomes, one each on group 2 and group 3, five on group 4, four on group 5, one on group 6 and three on group 7. The strongest yield QTL effects were on chromosomes 7AL and 7BL, due mainly to variation in grain numbers per ear. Three of the yield QTL clusters were largely site-specific, while four clusters were largely associated with one or other of the stress treatments. Three of the yield QTL clusters were coincident with the dwarfing gene Rht-B1 on 4BS and with the vernalisation genes Vrn-A1 on 5AL and Vrn-D1 on 5DL. Yields of each DHL were calculated for trial mean yields of 6 g plant-1 and 2 g plant-1 (equivalent to about 8 t ha-1 and 2.5 t ha-1, respectively), representing optimum and moderately stressed conditions. Analyses of these yield estimates using interval mapping confirmed the group-7 effects on yield and, at 2 g plant-1, identified two additional major yield QTLs on chromosomes 1D and 5A. Many of the yield QTL clusters corresponded with QTLs already reported in wheat and, on the basis of comparative genetics, also in rice. The implications of these results for improving wheat yield stability are discussed.
3. Identification of drought-inducible genes and differentially expressed sequence tags in barley. Diab AA, Teulat-Merah B, This D, Ozturk NZ, Benscher D, Sorrells ME. In: Theoretical and Applied Genetics, 2004, 109: 1417-1425.
Drought limits cereal yields in several regions of the world and plant water status plays an important role in tolerance to drought. To investigate and understand the genetic and physiological basis of drought tolerance in barley, differentially expressed sequence tags (dESTs) and candidate genes for the drought response were mapped in a population of 167 F8 recombinant inbred lines derived from a cross between 'Tadmor' (drought tolerant) and 'Er/Apm' (adapted only to specific dry environments). One hundred sequenced probes from two cDNA libraries previously constructed from drought-stressed barley (Hordeum vulgare L., var. Tokak) plants and 12 candidate genes were surveyed for polymorphism, and 33 loci were added to a previously published map. Composite interval mapping was used to identify quantitative trait loci (QTL) associated with drought tolerance including leaf relative water content, leaf osmotic potential, osmotic potential at full turgor, water-soluble carbohydrate concentration, osmotic adjustment, and carbon isotope discrimination. A total of 68 QTLs with a limit of detection score >=2.5 were detected for the traits evaluated under two water treatments and the two traits calculated from both treatments. The number of QTLs identified for each trait varied from one to 12, indicating that the genome contains multiple genes affecting different traits. Two candidate genes and ten differentially expressed sequences were associated with QTLs for drought tolerance traits.
4. Traits for improved drought tolerance of winter wheat in the UK . Foulkes MJ, Verma V, Sylvester-Bradley R, Weightman R, Snape JW. In: Proceedings of the 4th International Crop Science Congress. Brisbane, Australia, 2004. [Congress link]
5.The ability of wheat cultivars to withstand drought in UK conditions: formation of grain yield. Foulkes MJ, Scott RK, Sylvester-Bradley R. In: Journal of Agricultural Science, 2002, 138:153-169.
Experiments in three dry years, 1993/94, 1994/95 and 1995/96, on a medium sand at ADAS Gleadthorpe, England, tested responses of six winter wheat cultivars to irrigation of dry-matter growth, partitioning of dry matter to leaf, stem and ear throughout the season, and to grain at final harvest. Cultivars (Haven, Maris Huntsman, Mercia, Rialto, Riband and Soissons) were selected for contrasts in flowering date and stem soluble carbohydrate. Maximum soil moisture deficit (SMD) exceeded 140 mm in all years, with large deficits (>75 mm) from early June in 1994 and from May in 1995 and 1996. The main effects of drought on partitioning of biomass were for a decrease in the proportion of the crop as lamina in the pre-flowering period, and then earlier retranslocation of stem reserves to grains during the first half of grain filling. Restricted water availability decreased grain yield by 1.83 t/ha in 1994 (P<0.05), and with more prolonged droughts, by 3.06 t/ha in 1995 (P<0.001) and by 4.55 t/ha in 1996 (P<0.001). Averaged over the three years, grain yield responses of the six cultivars differed significantly (P<0.05). Rialto and Mercia lost only 2.8 t/ha compared with Riband and Haven which lost 3.5 t/ha. Losses for Soissons and Maris Huntsman were intermediate. In the two years with prolonged drought, the biomass depression was on average greater for Haven (6.0 t/ha) than for Maris Huntsman (4.2 t/ha) (P<0.05). Thus, the grain yield sensitivity of Haven to drought derived, in part, from a sensitivity of biomass growth to drought. Harvest index (HI; ratio of grain to above-ground dry matter at harvest) responses of the six cultivars to irrigation also differed (P<0.05) and contributed to the yield responses. The smallest decrease in HI of the six cultivars with restricted water availability was shown by Rialto (-0.033); this partially explained the drought resistance for this cultivar. The largest decrease was for Maris Huntsman (-0.072). The cultivars differed in flowering dates by up to 9 days but these were poorly correlated with grain yield responses to irrigation. Stem soluble carbohydrate at flowering varied amongst cultivars from 220 to 300 g/m2 in the unirrigated crop; greater accumulation appeared to be associated with better maintenance of HI under drought. It is concluded that high stem-soluble carbohydrate reserves could be used to improve drought resistance in the UK’s temperate climate, but that early flowering seems less likely to be useful.
6. Mapping quantitative trait loci for flag leaf senescence as a yield determinant in winter wheat under optimal and drought-stressed environments . Verma V, Foulkes MJ, Worland AJ, Sylvester-Bradley R, Caligari PDS, Snape JW In: Euphytica, 2004, 135:255-263.
The timing of flag leaf senescence (FLS) is an important determinant of yield under stress and optimal environments. A doubled haploid population derived from crossing the photoperiod-sensitive variety Beaver, with the photoperiod-insensitive variety Soissons, varied significantly for this trait, measured as the percent green flag leaf area remaining at 14 days and 35 days after anthesis. This trait also showed a significantly positive correlation with yield under variable environmental regimes. QTL analysis based on a genetic map derived from 48 doubled haploid lines using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers, revealed the genetic control of this trait. The coincidence of QTL for senescence on chromosomes 2B and 2D under drought-stressed and optimal environments, respectively, indicate a complex genetic mechanism of this trait involving the re-mobilisation of resources from the source to the sink during senescence.
7. Agronomic Effects from Chromosome Translocations 7DL.7Ag and 1BL.1RS in Spring Wheat. Singh RP, Huerta-Espino J, Rajaram S, Crossa J. In: Crop Science, 1998, 38:27–33.
In hexaploid wheat (Triticum aestivum L.) disease resistance genes transferred from alien sources are often associated with undesirable traits. Replicated trials using near-isogenic lines of spring wheat ‘Seri 82’ were conducted for 2 yr under non-moisture stress and simulated moisture stress conditions to determine the effects of the 7DL.7Ag and 1BL.1RS translocations [from Agropyron elongatum (Host) Beauv. and Secale cereale L., respectively] on grain yield and related traits. Mean grain yield of the 1B lines was significantly higher (3.2%) than that of the 1BL.1RS translocation lines in non-moisture stress trials, but not significantly higher in the moisture stress trials. The genotypes (1BL.1RS) were significantly lower than that of the geno-types without the 1BL.1RS translocation in non-moisture stress (3.2%) and moisture stress (5.2%) conditions. Incorporation of the 7DL.7Ag translocation caused a significant increase (9%) in biomass at harvest in non-moisture stress trials. The mean grain yields of the five highest yielding 7DL.7Ag lines were significantly higher (8.2%) than the reconstituted Seri 82 genotypes in non-moisture stress conditions and more than 16% lower under moisture stress. Lower grain yields of the 7DL.7Ag lines under moisture stress could be due to their excessive pre-heading biomass production. Several yield-related traits of the near-isogenic genotypes varied significantly. Presence of each translocation caused lateness and, when present together, the 1BL.1RS and 7DL.7Ag translocations delayed heading and maturity by 7 and 5 d, respectively. The genetic background of the recipient wheat can affect the utility of a translocation.
8. Root Biomass, Water-Use Efficiency, and Performance of Wheat-Rye Translocations of Chromosomes 1 and 2 in Spring Bread Wheat 'Pavon'. Ehdaie B, Whitkus RW, Waines JG. In: Crop Science, 2003, 43:710–-717.
Positive performance is reported for centric translocations of chromosome 1 of rye (Secale cereale L.) in bread wheat (Triticum aestivum L.). Objectives were to determine the effects of short arm translocations of rye chromosome 1 (1RS) derived from 'Kavkaz' winter wheat, in 'Pavon' spring wheat background, on root biomass, water-use efficiency, and agronomic performance. Pavon and its translocations were evaluated in glasshouse pot experiments in 1997 and 1998 and in field experiments in 1999 and 2000 under well-watered and droughted treatments. The 1RS translocations in Pavon delayed maturity, reduced plant height in some cases, and increased root biomass. Association between root biomass and grain yield was significant under droughted and under well-watered conditions. The 1RS translocations increased grain yield and grain weight, especially under well-watered field conditions. The overall mean grain yield was 4.066 Mg ha-1 for Pavon, 4.895 Mg ha-1 for 1RS.1AL, 4.503 Mg ha-1 for 1RS.1BL, and 4.632 Mg ha-1 for 1RS.1DL. The 1RS translocations, in general, were more tolerant to field environmental stresses than Pavon. These results encourage the development and use of the 1RS.1AL and 1RS.1DL translocations in wheat breeding programs.
9. Generation of PCR-based Markers for the Detection of Rye Chromatin in a Wheat Background. Koebner RMD. In: Theoretical and Applied Genetics, 1995, 90:740-745.
Oligonucleotide primers were developed to detect the presence of four rye sequences using a PCR assay. These assays give a rye-specific signal from wheat DNA template which contains various rye chromosomes or chromosome segments. The sequences identified were associated with the nucleolar organiser region, the 5s-Rrna-R1 locus, the telomere, and a widely dispersed, rye-specific repetitive element Ris-1. The primers amplified from the well-established loci Nor-R1 and 5s-Rrna-R1 on rye chromosome arm 1RS, and also located a 5s-Rrna locus on chromosome 3R. The telomere-associated sequence was present on every rye chromosome, and was also present, at a low copy number, in both wheat and barley. These assays will be particularly useful for introgression programmes aimed at reducing the rye content of the 1BL.1RS wheat-rye translocation. When multiplexed, the primers will enable a rapid, simultaneous assay for a number of dis tinct rye loci, which can be derived from a small portion of mature endosperm tissue.
10. Development of simple sequence repeat markers in rye (Secale cereale L.). Saal B, Wricke G. In: Genome, 1999, 42:964-972.
Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)n and (GT/CA)n dinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n (61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.