International Triticeae Mapping Initiative Population Research Articles

Analysis of contributors to grain yield in wheat at the individual quantitative trait locus level

AbstractIn wheat, strong genetic correlations have been found between grain yield (GY) and tiller number per plant (TN), fertile spikelet number per spike (FSN), kernel number per spike (KN) and thousand‐kernel weight (TKW). To investigate their genetic relationships at the individual quantitative trait locus (QTL) level, we performed both normal and multivariate conditional QTL analysis based on two recombinant inbred lines (RILs) populations. A total of 79 and 48 normal QTLs were identified in the International Triticeae Mapping Initiative (ITMI)/SHW‐L1 × Chuanmai 32 (SC) populations, respectively, as well as 55 and 35 conditional QTLs. Thirty‐two QTL clusters in the ITMI population and 18 QTL clusters in the SC population explained 0.9%–46.2% of phenotypic variance for two to eight traits. A comparison between the normal and conditional QTL mapping analyses indicated that FSN made the smallest contribution to GY among the four GY components that were considered at the QTL level. The effects of TN, KN and TKW on GY were stronger at the QTL level.

Conditional QTL mapping for waterlogging tolerance in two RILs populations of wheat

Waterlogging is a widespread limiting factor for wheat production throughout the world, specially irrigated and high rainfall environments. Only few studies reported QTLs for waterlogging tolerance. To identify quantitative trait loci (QTLs) for waterlogging tolerance, root dry weight index (RDWI), shoot dry weight index (SDWI), total dry weight index (TDWI) were measured at seedling stage in two unrelated recombinant inbred lines (RILs) populations. These populations were International Triticeae Mapping Initiative (ITMI) population ‘W7984 / Opata85’, and ‘SHW-L1 × Chuanmai 32’ (SC) population. Conditional QTL mapping and unconditional QTL mapping were studied to dissect the genetic relationship between TDWI and its components of SDWI and TDWI. Total of 36 QTLs for waterlogging tolerance in ITMI population and 10 QTLs in SC population were identified in present study. Of them, 17 alleles from synthetic hexaploid wheat ‘W7984’ and 3 alleles from synthetic hexaploid wheat ‘SHW-L1’ contribute positively to waterlogging tolerance. Combinations of conditional and unconditional mapping methods indicate that SDWI showed tighter genetic correlation with TDWI than RDWI. This QTL identification study and dissection provide theoretical basis and application foundation to Marker-assisted selection (MAS) of waterlogging tolerance improvement in wheat.

Identification and Molecular Characterization of Leaf Rust Resistance Gene Lr14a in Durum Wheat.

Leaf rust, caused by Puccinia triticina, is an important disease of durum wheat (Triticum turgidum subsp. durum) and only a few designated resistance genes are known to occur in this crop. A dominant leaf rust resistance gene in the Chilean durum cv. Llareta INIA was mapped to chromosome arm 7BL through bulked segregant analysis using the amplified fragment length polymorphism (AFLP) technique, and by mapping three polymorphic markers in the common wheat (T. aestivum) International Triticeae Mapping Initiative population. Several simple sequence repeat (SSR) markers, including Xgwm344-7B and Xgwm146-7B, were associated with the leaf rust resistance gene. Resistance response and chromosomal position indicated that this gene is likely to be Lr14a. The SSR markers Xgwm344-7B and Xgwm146-7B and one AFLP marker also differentiated common wheat cv. Thatcher from the near-isogenic line with Lr14a, as well as durum 'Altar C84' from durum wheat with Lr14a. This is the first report of the presence of Lr14a in durum wheat, although the gene originally was transferred from emmer wheat 'Yaroslav' to common wheat. Lr14a is also present in CIMMYT-derived durum 'Somateria' and effective against Mexican and other P. triticina races of durum origin. Lr14a should be deployed in combination with other effective leaf rust resistance genes to prolong its effectiveness in durum wheat.

Map-based analysis of genetic loci on chromosome 2D that affect glume tenacity and threshability, components of the free-threshing habit in common wheat (Triticum aestivum L.)

During the domestication of bread wheat (Triticum aestivum L.), evolutionary modifications that took place in seed dispersal mechanisms enhanced its suitability for agricultural production. One of these modifications involved the evolution of the free-threshing or hulless characteristic. In this study, we studied quantitative trait loci (QTL) affecting components of the free-threshing habit (threshability and glume tenacity) on chromosome 2D in a recombinant inbred line (RIL) population developed by the International Triticeae Mapping Initiative (ITMI) as well as the tenacious glumes 1 (Tg1) gene in F(2) progeny (CS/CS2D F(2)) of a cross between Chinese Spring and the 2D2 substitution line [Chinese Spring (Ae. tauschii 2D)]. In the ITMI population, two QTL affected threshability (QFt.orst-2D.1 and QFt.orst-2D.2) and their location coincided with QTL affecting glume tenacity (QGt.orst-2D.1 and QGt.orst-2D.2). In the CS/CS2D F(2) population, the location of QTL that affected glume tenacity (QGt.orst-2D.1), the size of a glume base scar after detachment (QGba.orst-2D), and Tg1 (12-cM interval between Xwmc112 and Xbarc168) also coincided. Map comparisons suggest that QFt-orst-2D.1, QGt.orst-2D.1, and QGba.orst-2D correspond to Tg1 whereas QFt.orst-2D.2 and QGt.orst-2D.2 appear to represent separate loci. The observation of coincident QTL for threshability and glume tenacity suggests that threshability is a function of glume adherence. In addition, the observation of the coincident locations of Tg1 and QTL for the force required to detach a glume and the size of a glume base scar after detachment suggests that Tg1's effect on both glume tenacity and threshability resides on its ability to alter the level of physical attachment of glumes to the rachilla of a spikelet.

Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population

Root-lesion nematode (Pratylenchus thornei) is a serious pathogen of wheat in many countries. The International Triticeae Mapping Initiative (ITMI) population of recombinant inbred lines (RILs) was assessed for resistance to P. thornei to determine the chromosome locations of the resistance genes. The ITMI population is derived from a cross between the resistant synthetic hexaploid wheat W-7984 and a susceptible bread wheat cultivar Opata 85. Two years of phenotypic data for resistance to P. thornei were obtained in replicated glasshouse trials. Quantitative trait locus (QTL) analysis was performed using available segregation and map data for 114 RILs. A QTL on chromosome 6DS showed consistent effects for reduced nematode numbers (partial resistance) across years and accounted for 11% and 23% of the phenotypic variation. A second QTL for P. thornei resistance on chromosome 2BS accounted for an additional 19% and 5%. Restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers associated with the QTLs are physically located in regions rich in major genes at the distal ends of the short chromosome arms of 6D and 2B. SSR markers with potential for marker-assisted selection of P. thornei resistance effective in different genetic backgrounds have been identified.

Microsatellite markers associated with two Aegilops tauschii-derived greenbug resistance loci in wheat

A new source of greenbug (Schizaphis graminum Rondani) resistance derived from Aegilops tauschii (Coss.) Schmal was identified in W7984, a synthetic hexaploid wheat line and one parent of the International Triticeae Mapping Initiative (ITMI) mapping population. Segregation analysis of responses to greenbug feeding in a set of recombinant inbred lines (RILs) identified a single, dominant gene governing the greenbug resistance in W7984, which was placed in chromosome arm 7DL by linkage analysis with molecular markers in the ITMI population. Allelism tests based on the segregation of responses to greenbug feeding in F2 and testcross plants revealed that the greenbug resistance in W7984 and Largo, another synthetic line carrying the greenbug resistance gene Gb3, was controlled by different but linked loci. Using the ITMI reference map and a target mapping strategy, we have constructed a microsatellite map of Gb3 in a mapping population of 130 F7 RILs from Largo x TAM 107 and identified one marker (Xwmc634) co-segregating with Gb3 and four markers (Xbarc76, Xgwm037, Xgwm428 and Xwmc824) closely linked with Gb3. Deletion mapping of selected microsatellite markers flanking the Gb3 locus placed this resistance gene into the distal 18% region of 7DL. Comparative mapping in the ITMI and Largo x TAM 107 populations using the same set of microsatellite markers provided further evidence that greenbug resistance in W7984 and Largo is conditioned by two different loci. We suggest that the greenbug resistance gene in W7984 be designated Gb7. The microsatellite map of Gb3 constructed from this study should be a valuable tool for marker-assisted selection of Gb3-conferred greenbug resistance in wheat breeding.

Genetic basis of pre-harvest sprouting tolerance using single-locus and two-locus QTL analyses in bread wheat.

Quantitative trait loci (QTL) analysis for pre-harvest sprouting tolerance (PHST) in bread wheat was conducted following single-locus and two-locus analyses, using data on a set of 110 recombinant inbred lines (RILs) of the International Triticeae Mapping Initiative population grown in four different environments. Single-locus analysis following composite interval mapping (CIM) resolved a total of five QTLs with one to four QTLs in each of the four individual environments. Four of these five QTLs were also detected following two-locus analysis, which resolved a total of 14 QTLs including 8 main effect QTLs (M-QTLs), 8 epistatic QTLs (E-QTLs) and 5 QTLs involved in QTL x environment (QE) or QTL x QTL x environment (QQE) interactions, some of these QTLs being common. The analysis revealed that a major fraction (76.68%) of the total phenotypic variation explained for PHST is due to M-QTLs (47.95%) and E-QTLs (28.73%), and that only a very small fraction of variation (3.24%) is due to QE and QQE interactions. Thus, more than three-quarters of the genetic variation for PHST is fixable and would contribute directly to gains under selection. Two QTLs that were detected in more than one environment and at LOD scores above the threshold values were located on 3BL and 3DL presumably in the vicinity of the dormancy gene TaVp1. Another QTL was found to be located on 3B, perhaps in close proximity to the R gene for red grain colour. However, these associations of QTLs for PHST with genes for dormancy and grain colour are only suggestive. The results obtained in the present study suggest that PHST is a complex trait controlled by large number of QTLs, some of them interacting among themselves or with the environment. These QTLs can be brought together through marker-aided selection, leading to enhanced PHST.

Identification and mapping of genetic loci affecting the free-threshing habit and spike compactness in wheat ( Triticum aestivum L.).

Recombinant inbred lines of the International Triticeae Mapping Initiative (ITMI) mapping population were used to localize genetic loci that affect traits related to the free-threshing habit (percent threshability, glume tenacity, and spike fragility) and to spike morphology (spike length, spikelet number, and spike compactness) of wheat ( Triticum aestivum L.). The ITMI population was planted in three environments during 1999 and 2000, and phenotypic and genotypic data were used for composite interval mapping. Two quantitative trait loci (QTL) that consistently affected threshability-associated traits were localized on chromosomes 2D and 5A. Coincident QTL on the short arm of 2D explained 44% of the variation in threshability, 17% of the variation in glume tenacity, and 42% of the variation in rachis fragility. QTL on chromosomes 2D probably represent the effect of Tg, a gene for tenacious glumes. Coincident QTL on the long arm of 5A explained 21% and 10% of the variation in glume tenacity and rachis fragility, respectively. QTL on 5A are believed to represent the effect of Q. Overall, free-threshing-related characteristics were predominantly affected by Tg and to a lesser extent by Q. Other QTL that were significantly associated with threshability-related traits in at least one environment were localized on chromosomes 2A, 2B, 6A, 6D, and 7B. Four QTL on chromosomes 1B, 4A, 6A, and 7A consistently affected spike characteristics. Coincident QTL on the short arm of chromosome 1B explained 18% and 7% of the variation in spike length and spike compactness, respectively. QTL on the long arm of 4A explained 11%, 14%, and 12% of the variation in spike length, spike compactness, and spikelet number, respectively. A QTL on the short arm of 6A explained 27% of the phenotypic variance for spike compactness, while a QTL on the long arm of 7A explained 18% of the variation in spikelet number. QTL on chromosomes 1B and 6A appear to affect spike dimensions by modulating rachis internode length, while QTL on chromosomes 4A and 7A do so by affecting the formation of spikelets. Other QTL that were significantly associated with spike morphology-related traits, in at least one environment, were localized on chromosomes 2B, 3A, 3D, 4D, and 5A.

Molecular Marker Mapping of Leaf Rust Resistance Gene Lr46 and Its Association with Stripe Rust Resistance Gene Yr29 in Wheat

ABSTRACT Leaf and stripe rusts, caused by Puccinia triticina and P. striiformis, respectively, are globally important fungal diseases of wheat that cause significant annual yield losses. A gene that confers slow rusting resistance to leaf rust, designated as Lr46, has recently been located on wheat chromosome 1B. The objectives of our study were to establish the precise genomic location of gene Lr46 using molecular approaches and to determine if there was an association of this locus with adult plant resistance to stripe rust. A population of 146 F(5) and F(6) lines produced from the cross of susceptible 'Avocet S' with resistant 'Pavon 76' was developed and classified for leaf rust and stripe rust severity for three seasons. Using patterns of segregation for the two diseases, we estimated that at least two genes with additive effects conferred resistance to leaf rust and three to four genes conferred resistance to stripe rust. Bulked segregant analysis and linkage mapping using amplified fragment length polymorphisms with the 'Avocet' x 'Pavon 76' population, F(3) progeny lines of a single chromosome recombinant line population from the cross 'Lalbahadur' x 'Lalbahadur (Pavon 1B)', and the International Triticeae Mapping Initiative population established the genomic location of Lr46 at the distal end of the long arm of wheat chromosome 1B. A gene that is closely linked to Lr46 and confers moderate levels of adult plant resistance to stripe rust is identified and designated as Yr29.