Recombinant Inbred Chromosome Lines Research Articles

Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat.

New molecular markers were developed and mapped to the FHB resistance QTL region in high resolution. Micro-collinearity of the QTL region with rice and Brachypodium was revealed for a better understanding of the genomic region. The wild emmer wheat (Triticum dicoccoides)-derived Fusarium head blight (FHB) resistance quantitative trait locus (QTL) Qfhs.ndsu-3AS previously mapped to the short arm of chromosome 3A (3AS) in a population of recombinant inbred chromosome lines (RICLs). This study aimed to attain a better understanding of the genomic region harboring Qfhs.ndsu-3AS and to improve the utility of the QTL in wheat breeding. Micro-collinearity of the QTL region with rice chromosome 1 and Brachypodium chromosome 2 was identified and used for marker development in saturation mapping. A total of 42 new EST-derived sequence tagged site (STS) and simple sequence repeat (SSR) markers were developed and mapped to the QTL and nearby regions on 3AS. Further comparative analysis revealed a complex collinearity of the 3AS genomic region with their collinear counterparts of rice and Brachypodium. Fine mapping of the QTL region resolved five co-segregating markers (Xwgc1186/Xwgc716/Xwgc1143/Xwgc501/Xwgc1204) into three distinct loci proximal to Xgwm2, a marker previously reported to be closely linked to the QTL. Four other markers (Xwgc1226, Xwgc510, Xwgc1296, and Xwgc1301) mapped farther proximal to the above markers in the QTL region with a higher resolution. Five homozygous recombinants with shortened T. dicoccoides chromosomal segments in the QTL region were recovered by molecular marker analysis and evaluated for FHB resistance. Qfhs.ndsu-3AS was positioned to a 5.2cM interval flanked by the marker Xwgc501 and Xwgc510. The recombinants containing Qfhs.ndsu-3AS and new markers defining the QTL will facilitate utilization of this resistance source in wheat breeding.

Validation of QTL for Grain Yield‐Related Traits on Wheat Chromosome 3A Using Recombinant Inbred Chromosome Lines

ABSTRACTPreviously, quantitative trait loci (QTLs) for grain yield (GYLD) and yield‐related traits were identified by using a population of recombinant inbred chromosome lines (RICLs) developed from the wheat (Triticum aestivum L.) cultivar Cheyenne (CNN) and its substitution line CNN(WI3A), in which the 3A chromosome of cultivar Wichita (WI) was substituted for CNN chromosome 3A. Our objectives were to identify and validate the QTL previously identified in CNN(RICLs3A), using the mirror population WI(RICLs3A). A population of 90 WI(RICLs3A) was used to evaluate GYLD, 1000‐kernel weight (TKW), kernels per spike (KPS), kernels per square meter (KPSM), spikes per square meter (SPSM), grain volume weight (GVW), plant height (PHT), and anthesis date (AD). Data were collected from replicated trials grown in six Nebraska environments from 2008 to 2009. Twelve QTL for GYLD, TKW, KPS, SPSM, GVW, AD, and PHT were detected. The phenotypic variance explained by these QTL ranged from 12% for SPSM to 53% for GVWT. Most of the QTLs were co‐localized in one or two regions of chromosome 3A. The major grain yield QTL (QGyld.neb.3A.1) detected in the combined analysis explained 19% of the phenotypic variance and the substitution of CNN alleles for WI alleles decreased grain yield. Using a different genetic background, this study confirmed most of the GYLD and yield‐related QTL reported in previous RICLs3A mapping studies on chromosome 3A of winter wheat evaluated in Nebraska.

Understanding grain yield: it is a journey, not a destination

Approximately 20 years ago, we began our efforts to understand grain yield in winter wheat using chromosome substitution lines between Cheyenne (CNN) and Wichita (WI). We found that two chromosome substitutions, 3A and 6A, greatly affected grain yield. CNN(WI3A) and CNN(WI6A) had 15 to 20% higher grain yield than CNN, whereas WI(CNN3A) and WI(CNN6A) had 15 to 20% lower grain yield than WI. The differences in grain yield are mainly expressed in higher yielding environments (e.g. eastern Nebraska) indicating genotype by environment interactions (G × E). In studies using hybrid wheat, the gene action for grain yield on these chromosomes was found to be mainly controlled by additive gene action. In subsequent studies, we developed recombinant inbred chromosome lines (RICLs) using monosomics or doubled haploids. In extensive studies we found that two regions on 3A affect grain yield in the CNN(RICLs-3A) with the positive QTLs coming from WI. In WI(RICLs-3A), we found a main region on 3A that affected grain yield with the negative QTL coming from CNN. The 3A region identified using WI(RICLs-3A) coincided with one of the regions previously identified in CNN(RICLs-3A). As expected the QTLs have their greatest effect in higher-yielding environments and also exhibit QTL × E. Using molecular markers on chromosomes 3A and 6A, the favorable alleles on 3A in Wichita may be from Turkey Red, the original hard red winter wheat in the Great Plains and presumably the original source of the favorable alleles. Cheyenne, a selection from Crimea, did not have the favorable alleles. In studying modern cultivars, many high yielding cultivars adapted to eastern Nebraska have the WI-allele indicating that it was selected for in breeding higher yielding cultivars. However, some modern cultivars adapted to western Nebraska where the QTL has less effect retain the CNN-allele, presumably because the allele has less effect (is less important in improving grain yield). In addition many modern cultivars have neither the WI-allele, nor the CNN-allele indicating we have diversified our germplasm and new alleles have been brought into the breeding program in this region.

A quantitative trait locus on chromosome 5B controls resistance of Triticum turgidum (L.) var. diccocoides to Stagonospora nodorum blotch

Stagonospora nodorum blotch (SNB) is an important foliar disease of durum wheat (Triticum turgidum var. durum) worldwide. The combined effects of SNB and tan spot, considered as components of the leaf spotting disease complex, result in significant damage to wheat production in the northern Great Plains of North America. The main objective of this study was the genetic analysis of resistance to SNB caused by Phaeosphaeria nodorum in tetraploid wheat, and its association with tan spot caused by Pyrenophora tritici-repentis race 2. The 133 recombinant inbred chromosome lines (RICL) developed from the cross LDN/LDN(Dic-5B) were evaluated for SNB reaction at the seedling stage under greenhouse conditions. Molecular markers were used to map a quantitative trait locus (QTL) on chromosome 5B, explaining 37.6% of the phenotypic variation in SNB reaction. The location of the QTL was 8.8 cM distal to the tsn1 locus coding for resistance to P. tritici-repentis race 2. The presence of genes for resistance to both SNB and tan spot in close proximity in tetraploid wheat and the identification of molecular markers linked to these genes or QTLs will be useful for incorporating resistance to these diseases in wheat breeding programs.

The effects of chromosomes 3A and 3B on resistance to Fusarium head blight in tetraploid wheat.

Fusarium head blight (FHB) caused by Fusarium graminearum is one of the most destructive diseases of wheat in areas where the weather is warm and humid after heading. Previous studies indicate that the level of resistance to FHB varies not only among wheat cultivars but also among some of their wild relatives. No accession, however, has yet been identified to be completely immune to FHB among the Gramineae. It is known that durum wheat (Triticum turgidum L. conv. durum) is consistently more susceptible to FHB than common wheat (T. aestivum L.). The importance of the D genome in conferring resistance to FHB has been emphasized. Meanwhile, recent studies using molecular markers report effective QTLs on chromosome 3BS in a hexaploid population and on 3A in tetraploid recombinant inbred chromosome lines. In this study, we performed an evaluation of the effects of homoeologous group 3 chromosomes of T. turgidum ssp. dicoccoides on resistance to FHB using a set of chromosome substitution lines of a durum wheat cultivar 'Langdon'. The accession of T. turgidum ssp. dicoccoides examined in this study was more susceptible for Type II resistance (resistance to spread of FHB in the head) than 'Langdon'. Both of the chromosome substitution lines of 3A and 3B showed the same level of resistance with 'Langdon', but bleaching of the heads was completely prevented in the substitution lines of chromosome 3A without relationship to rachis fragility. It was concluded that the chromosome 3A of T. turgidum ssp. dicoccoides carries resistance gene(s) to head bleaching caused by FHB.

Using Environmental Covariates to Explain Genotype × Environment and QTL × Environment Interactions for Agronomic Traits on Chromosome 3A of Wheat

Genotype × environment interactions (GEI) and quantitative trait loci × environment interactions (QEI) are known to influence the expression of agronomic performance traits in wheat. The aim of this study was to provide biological and environmental explanations for large GEI and QEI known to affect the expression of genes on chromosome 3A of wheat (Triticum aestivum L.). Agronomic performance and molecular marker data available for a population of chromosome 3A recombinant inbred chromosome lines (RICLs‐3A) in seven environments was used along with environmental covariate data to construct individual factorial regressions to explain GEI and QEI. Precipitation and temperature before anthesis had the greatest influence on agronomic performance traits for the RICLs‐3A, and explained a sizeable portion of the total GEI for those traits. Individual molecular marker × environmental covariate interactions explained a large portion of the total marker × environment interactions for several agronomic traits. Seventy‐six percent of the QEI for a major grain yield quantitative trait locus (QTL) was explained by the effect of temperature during preanthesis growth on dissimilar QTL genotype differentials across testing environments. Environmental covariates provided a strong basis for explaining QEI using marker × environmental covariate interactions.

Mapping genes for grain protein concentration and grain yield on chromosome 5B of Triticum turgidum (L.) var. dicoccoides

Grain protein concentration (GPC) is an important quality factor in durum wheat [Triticum turgidum (L.) var. durum]. Due to the strong environmental influence on GPC, molecular markers linked to quantitative trait loci (QTL) affecting GPC have the potential to be valuable in wheat breeding programs. Various quantitative traits in a population of 133 recombinant inbred chromosome lines were studied in replicated trials at three locations in North Dakota. Segregation for GPC, 1000-kernel weight, gluten strength, heading date, and plant height was observed. By relating phenotypic data to a linkage map obtained from the same population, three QTL affecting GPC, and one affecting yield were identified. The genotypic coefficients of determination for both traits were high.

Identification of QTLs and Environmental Interactions Associated with Agronomic Traits on Chromosome 3A of Wheat

Genetic analyses of complex traits in wheat (Triticum aestivum L.) are facilitated by the availability of unique genetic tools such as chromosome substitution lines and recombinant inbred chromosome lines (RICLs) which allow the effects of genes on single chromosomes to be studied individually. Chromosome 3A of ‘Wichita’ is known to contain alleles at quantitative trait loci (QTLs) that influence variation in grain yield and agronomic performance traits relative to alleles of ‘Cheyenne’. To determine the number, location, and environmental interactions of genes related to agronomic performance on chromosome 3A, QTL and QTL × environment analyses of 98 RICLs‐3A were conducted in seven locations across Nebraska from 1999 through 2001. QTLs were detected for seven of eight agronomic traits measured and generally localized to three regions of chromosome 3A. QTL × environment interactions were detected for some QTLs and these interactions were caused by changes in magnitude and crossover interactions. Major QTLs for kernels per square meter and grain yield were associated within a 5‐centimorgan (cM) interval and appeared to represent a single QTL with pleiotropic effects. This particular QTL displayed environmental interactions caused by changes in magnitude, wherein the positive effect of the Wichita QTL allele was larger in higher yielding environments.

Genetic dissection of a major Fusarium head blight QTL in tetraploid wheat.

The devastating effect of Fusarium head blight (FHB) caused by Fusarium graminearum has led to significant financial losses across the Upper Midwest of the USA. These losses have spurred the need for research in biological, chemical, and genetic control methods for this disease. To date, most of the research on FHB resistance has concentrated on hexaploid wheat (Triticum aestivum L.) lines originating from China. Other sources of resistance to FHB would be desirable. One other source of resistance for both hexaploid wheat and tetraploid durum wheat (T. turgidum L. var. durum) is the wild tetraploid, T. turgidum L. var. dicoccoides (T. dicoccoides). Previous analysis of the 'Langdon'-T. dicoccoides chromosome substitution lines, LDN(Dic), indicated that the chromosome 3A substitution line expresses moderate levels of resistance to FHB. LDN(Dic-3A) recombinant inbred chromosome lines (RICL) were used to generate a linkage map of chromosome 3A with 19 molecular markers spanning a distance of 155.2 cM. The individual RICL and controls were screened for their FHB phenotype in two greenhouse seasons. Analysis of 83 RICL identified a single major quantitative trait locus, Qfhs.ndsu-3AS, that explains 37% of the phenotypic or 55% of the genetic variation for FHB resistance. A microsatellite locus, Xgwm2, is tightly linked to the highest point of the QTL peak. A region of the LDN (Dic-3A) chromosome associated with the QTL for FHB resistance encompasses a 29.3 cM region from Xmwg14 to Xbcd828.

Correcting for Classification Errors when Estimating the Number of Genes Using Recombinant Inbred Chromosome Lines

Techniques based on intercultivar chromosome substitution lines in wheat (Triticum aestivum L.) have been used to identify and locate the genes controlling quantitative traits on a specific chromosome. For a particular trait, the number of segregating loci affecting differences between two parental lines are generally determined by the frequency distribution of recombinant inbred chromosome lines (RICLs). Recombinant inbred chromosome lines are the inbred progeny of crosses between a chromosome substitution line and its parent cultivar. The determination of the presence and the number of segregating loci becomes difficult (i) when the distribution exhibits no clear discrete classes, (ii) when there is a considerable chance of misclassifying lines into parental and recombinant types, and (iii) when loci are linked. We describe an approach to estimate the number of segregating loci responsible for the difference between a chromosome substitution line and parental cultivar using the derived RICLs when classification errors are likely. We also discuss the effects of linked loci on the estimates. The method was used to estimate the number of genes on chromosome 3A controlling grain yield, kernels spike−1, kernel weight, spikes m−2, grain volume weight, plant height and anthesis date in wheat.

Molecular Mapping of Loci for Agronomic Traits on Chromosome 3A of Bread Wheat

ABSTRACTChromosome 3A of bread wheat (Triticum aestivum L.) cultivar ‘Wichita’ (WI) was previously found to differ from that of ‘Cheyenne’ (CNN) for genes affecting a number of agronomically important traits such as grain yield (GYLD), kernel number spike−1 (KPS), 1000‐kernel weight (TKWT), spike number m−2 (SPSM), grain volume weight (GVWT), plant height (PHT), and anthesis date (influenced by Eps locus). This study was designed to map the Eps locus and to identify regions of chromosome 3A of wheat associated with agronomic traits. A population of 3A recombinant inbred chromosome lines (RICLs‐3A) was previously evaluated in replicated field trials. Thirteen RFLPs and one morphological marker locus, Eps, were used to develop a genetic linkage map and to identify QTLs associated with agronomic traits. Individual loci explained from 8.9 to 38.2% of the total phenotypic variation for the measured traits. The major locus Eps was mapped distal to an RFLP marker locus Xcdo549 on the short arm of chromosome 3A and explained 38.2% of the total phenotypic variation for PHT, and 17.4% for both KPS and TKWT. Additional QTLs for PHT, TKWT, and KPS were identified on the chromosome. A QTL for SPSM on the long arm of chromosome 3A was tightly linked to QTL for PHT and KPS. QTLs for GYLD were identified only in a few individual environments whereas no QTL was detected for GVWT. No epistasis was detected between markers associated with QTLs. The QTLs identified across environments were consistent in all or most environments, hence should be useful in future marker assisted selection programs for breeding wheat cultivars.

Genetic Analyses of Agronomic Traits Controlled by Wheat Chromosome 3A

Previous studies with chromosome substitution lines between hard red winter wheat (Triticum aestivum L.) cultivars Cheyenne (CNN) and Wichita (WI) identified genes on chromosome 3A of WI which affect grain yield, yield components, grain volume weight, plant height, and anthesis date. This study was conducted to determine if the trait variation caused by chromosome 3A could be explained by major or minor gene segregation and if these genes are pleiotropic, linked, or independent on the chromosome. A population of recombinant inbred chromosome lines for chromosome 3A (RICLs‐3A), developed between CNN and a chromosome substitution line CNN(WI3A), was evaluated in multi‐location field trials in 3 yr. Our results indicate significant differences (P ≤ 0.05) between parental lines and among RICLs for grain yield, 1000‐kernel weight, plant height, and anthesis date, but not for kernel number per spike, spike number per square meter, and grain volume weight. A 1:1 genetic ratio for anthesis date suggested the presence of a single segregating locus controlling the trait. None of the other agronomic traits could be separated into unequivocal groups and hence, major genes were not detected. This indicates that the traits were controlled either by several genes or few genes with enough environmental influence, or both, to obscure their effects. Significant correlations and possible crossover products between anthesis date, plant height, and 1000‐kernel weight suggest that these traits were controlled either by linked gene(s) or by pleiotropic genes with additional genes affecting one of the traits.