Wheat Recombinant Inbred Lines Research Articles

Proteomic analysis of wheat recombinant inbred lines: Variations in prolamin and dough rheology

To investigate the impact of the 1BL.1RS translocation on dough strength and to understand how 1BL.1RS genotypes may overcome the loss of Glu-B3 and Gli-B1, proteomic profiles of 16 doubled haploid (DH) lines of similar glutenin composition but of different strength, as measured by Chopin's alveograph, were compared. The results showed that 32 spots, mainly prolamins, were differentially expressed and that five others were specific to high-strength DH lines. The identification and quantification of the prolamin fractions on the two-dimensional (2D) electrophoresis gels demonstrated that the high-molecular weight glutenin sub-unit (HMW-GS) were up-regulated by 25% in 1BL.1RS DH lines, even though the corresponding genes were not located on the missing 1BS chromosome. The γ-gliadins were also up-regulated (by 36%) in such lines to counterbalance, to some extent, the loss of LMW-GS of Glu-B3. The polymeric prolamin fractions also accumulated in high-tenacity lines and decreased in high-extensibility lines confirming the role of the inter-chain disulfide bonds in resistance to deformation. In contrast, the monomeric fraction of α-gliadin favored extensibility and decreased tenacity by increasing the accumulation (+12%) of α-gliadins in high-extensibility lines; the Gli-A1 allele of the parent Toronit was found to be more abundant when compared to the Gli-A1 allele of parent 211.12014.

Identification of micro satellite markers on chromosomes of bread wheat showing an association with karnal bunt resistance

A set of 104 wheat recombinant inbred lines developed from a cross between parents resistant (HD 29) and susceptible (WH 542) to karnal bunt (caused by Neovossia indica) were screened and used to identify SSR markers linked with resistance to karnal bunt as these would allow indirect marker assisted selection of karnal bunt resistant genotypes. The two parents were analysed with 46 SSR primer pairs. Of these, 15 (32%) were found polymorphic between the two parental genotypes. Using these primer pairs, we carried out bulked segregate analysis on two bulked DNAs, one obtained by pooling DNA from 10 karnal bunt resistant recombinant inbred lines and the other similarly derived by pooling DNA from 10 karnal bunt susceptible recombinant inbred lines. Two molecular markers, Xgwm 337-1D and Xgwm 637-4A showed apparent linkage with resistance to karnal bunt. This was confirmed following selective genotyping of individual recombinant inbred lines included in the bulks. These markers may be useful in marker assisted selection for karnal bunt resistance in wheat.

Mapping diploid wheat homologues of Arabidopsis seed ABA signaling genes and QTLs for seed dormancy

Abscisic acid (ABA) sensitivity in embryos is one of the key factors in the seed dormancy of wheat. Many ABA signaling genes have been isolated in Arabidopsis, while only a few wheat homologues have been identified. In the present study, diploid wheat homologues to Arabidopsis ABA signaling genes were identified by in silico analysis, and mapped them using a population of diploid wheat recombinant inbred lines derived from a cross between Triticum monococcum (Tm) and T. boeoticum (Tb). Four diploid wheat homologues, TmVP1, TmABF, TmABI8 and TmERA1 were located on chromosome 3A(m) and TmERA3 was on the centromere region of chromosome 5A(m). In two consecutive year trials, one major QTL on the long arm of 5A(m), two minor QTLs on the long arm of 3A(m) and one minor QTL on the long arm of 4A(m) were detected. The 5A(m) QTL explained 20-27% of the phenotypic variations and the other three QTLs each accounted for approximately 10% of the phenotypic variations. Map positions of the loci of TmABF and TmABI8 matched the LOD peaks of the two QTLs on 3A(m), indicating that these two homologues are possible candidate genes for seed dormancy QTLs. Moreover, we have found two SNPs result in amino acid substitutions in TmABF between Tb and Tm. Comparison of the marker positions of QTLs for seed dormancy of barley revealed that the largest QTL on 5A(m) may be orthologous to the barley seed dormancy QTL, SD1, whereas there seems no orthologous QTL to the corresponding barley SD2 locus.

Identification of RAPD markers linked to the karnal bunt resistance genes in wheat

A set of 104 wheat recombinant inbred lines (RILs) obtained from a cross between parents resistant (HD 29) and susceptible (WH 542) to karnal bunt (KB) (caused by Neovossia indica) were screened and used to identify random amplified polymorphic DNA (RAPD) markers linked with resistance to karnal bunt as these would allow indirect marker assisted selection of KB resistant genotypes. The two parents were analysed with 92 RAPD primers. A total of 65 primers proved functional by giving scorable polymerase chain reaction (PCR) products. Of these, 21 (32 %) primers detected polymorphism between the two parental genotypes. Using these primers, bulked segregant analysis was carried out on two bulk DNAs, one obtained by pooling DNA from 10 KB resistant RILs and the other similarly derived by pooling 10 KB susceptible RILs. One marker, OPM-20 showed apparent association with resistance to KB. This was confirmed following selective genotyping of individual RILs included in the bulks.

Analysis of preharvest sprouting in three Brazilian wheat populations

The objective of this work was to evaluate the possibility of obtaining recombinant inbred wheat lines more resistant to preharvest sprouting, independently of colour genes, in three red-grained Brazilian wheat populations. The results showed statistical significance among lines within all populations, which presented a normal distribution and transgressive segregation for preharvest sprouting. The normal distribution of the lines from all red-grained populations suggests that sprouting, excluding the genes expressing seed coat pigmentation, is, probably, controlled by many genes. These findings also indicate that it may be possible to improve resistance to preharvest sprouting, independently of the colour genes.

Detection and mapping of QTL for earliness components in a bread wheat recombinant inbred lines population

Earliness, an adaptative trait and factor of variation for agronomic characters, is a major trait in plant breeding. Its constituent traits, photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE), are largely under independent genetic controls. Mapping of major genes and quantitative trait loci (QTL) controlling these components is in progress. Most of the studies focusing on earliness considered it as a whole or through one (or two) of its components. The purpose of this study was to detect and map QTL for the three traits together through an experimental design combining field trials and controlled growth conditions. QTL were mapped in a population of F(7) recombinant inbred lines derived by single-seed descent from a cross between two French varieties, 'Renan' and 'Recital'. A map was previously constructed, based on 194 lines and 254 markers, covering about 77% of the genome. Globally, 13 QTL with a LOD>2.5 were detected, of which four control PS, five control VR and four control IE. Two major photoperiod sensitive QTL, together explaining more than 31% of the phenotypic variation, were mapped on chromosomes 2B and 2D, at the same position as the two major genes Ppd-B1 and Ppd-D1. One major VR QTL explaining (depending on the year) 21.8-39.6% of the phenotypic variation was mapped on 5A. Among the other QTL, two QTL of PS and VR not referenced so far were detected on 5A and 6D, respectively. A VR QTL already detected on 2B in a connected population was confirmed.

Quantitative trait loci for resistance to Fusarium head blight in recombinant inbred wheat lines from the cross Huapei 57-2 / Patterson

Fusarium head blight (FHB), primarily caused by Fusarium graminearum in North America, often results in significant losses in yield and grain quality of wheat (Triticum aestivum L.). Evaluation of FHB resistance is laborious and can be affected by environmental conditions. The development of DNA markers associated with FHB quantitative trait loci (QTL) and their use in breeding programs could greatly enhance selection. The objective of this study was to identify the location and effect of QTLs for FHB resistance using simple sequence repeat (SSR) markers. A population of wheat recombinant inbred lines derived from the cross ‘Huapei57-2’/‘Patterson’ was characterized for type II resistance in one field experiment and two tests under controlled conditions in the greenhouse. Bulked segregant analysis followed by QTL mapping was used to identify the major segregating QTLs. Results indicate that ‘Huapei 57-2’ may have the same resistance allele as ‘Sumai3’ at a QTL located on the short arm of chromosome 3B. Other QTLs of lower effect size were identified on the long arm of 3Band on chromosomes 3A and 5B. Our findings along with results from other studies demonstrate that the effect of the QTL on3BS is large and consistent across a wide range of genetic backgrounds and environments. Pyramiding this QTL with other FHB QTLs using marker-assisted selection should be effective in improving FHB resistance in a wheat breeding program.

Mapping of a resistance gene effective against Karnal bunt pathogen of wheat.

A set of 130 wheat recombinant inbred lines (RILs) developed from a cross between parents susceptible (WL711) and resistant (HD29) to Karnal bunt (caused by Tilletia indica), were screened for 3 years with the pathogen populations prevalent in northern India. When 90 simple sequence repeats (SSRs) and 81 amplified fragment length polymorphism (AFLP) loci were mapped on the RILs, markers on chromosomes 2A, 4B and 7B accounted collectively for about one-third of the variation in the disease reaction. The genomic region of largest effect, identified on the long arm of chromosome 4B, reduced Karnal bunt disease by half in three different experiments and accounted for up to 25% of the phenotypic variation for KB reaction. A closely linked SSR marker, GWM538, may be useful in marker-assisted selection for Karnal bunt resistance in wheat.

RFLP mapping of resistance to chlorosis induction by Pyrenophora tritici-repentis in wheat

Tan spot, caused by Pyrenophora tritici-repentis, is an economically important disease in major wheat production areas. The fungus can produce two genetically distinct symptoms on leaves of susceptible wheat genotypes: tan necrosis (nec) and extensive chlorosis (ch1). Our objectives were to determine the number of genes conditioning resistance to tan spot in a population of wheat recombinant inbred lines, and map the chromosomal location of the resistance genes using RFLPs. Conidia produced by the P. tritici-repentis isolate Pti2 (nee + chl +) were used to inoculate seedlings of 135 recombinant inbred lines derived from the cross of the synthetic hexaploid wheat W-7984 with Opata 85. A subset of the population was inoculated with conidia produced by the isolates D308 (nec - chl +) and 86-124 (nec + chl-). Inoculated seedlings were rated on a scale of 1 to 5 based on lesion type. Necrosis-inducing culture filtrate produced by the isolate 86-124 was also used to screen the entire population. A map consisting of 532 markers was employed to identify significant associations between marker loci and tan spot resistance. The entire population was insensitive to culture filtrate produced by the isolate 86-124, and the entire subset was resistant to conidial inoculation of the same isolate. The population segregated for reaction to isolates D308 and Pti2, indicating that this population segregates for resistance to extensive chlorosis only, and not to tan necrosis. RFLP analysis indicated the presence of a gene with a major effect in 1AS, a gene with a minor effect in 4AL, and an interaction between the 1AS gene and a gene in 2DL. Together, these loci explained 49.0% of the variation in this population for resistance to tan spot produced by the isolate Pti2. Two regions one in 1BL and one in 3BL, were significantly associated with resistance to extensive chlorosis, but were not significant in the multiple regression model. It should be feasible to introgress these resistance loci into adapted genetic backgrounds by using a marker-assisted selection scheme.

Responses of Recombinant Inbred Lines of Wheat to Saline Irrigations: Milling and Baking Qualities

Disposal of salinized drainage water is a problem in the irrigated San Joaquin Valley of California and it has been proposed that this water could be used judiciously in the culture of wheat Triticum aestivum L.). This may require breeding of cultivars specifically for this cropping system and the effects of saline irrigation on end‐use quality may be affected. These considerations were addressed in a field study where salinity concentration of irrigation water was controlled and water uniformly applied over test plots. Two agronomically desirable cultivars, Anza and Cajeme 71, and 43 random recombinant inbred lines derived from their hybrid were studied for two successive years with two N fertilization levels and three salinity levels. Nitrogen effects were minimal in this study because of a high level of basal N in the experimental site. Wheat flour quality and baking performance were improved by saline irrigation in the first year, but in the second year, when grain filling was poor, quality was adversely affected by salinity. High‐molecular‐weight glutenin alleles from Cajeme 71 at the Glu‐l locus were associated additively with improved flour protein content (Glu‐Al, Glu‐Dl), breadloaf volume (Glu‐Bl), and SDS sedimentation (Glu‐Dl). There was little or no interaction of the Glu‐l alleles with salinity for flour protein content and mixing time. Only one epistatic interaction effect out of 80 tested was significant (αABD for bake water absorption at high salinity in 1986). The additive effects were generally similar at the two salinity levels although interactions were detected which were less than 10% of the phcnorypic variance.

Use of recombinant inbred lines of wheat for study of associations of high-molecular-weight glutenin subunit alleles to quantitative traits

Recombinant inbred lines (RILs) derived by single plant descent to F8 from a hybrid of Anza, a low-quality cultivar, and Cajeme 71, a high-quality cultivar, differed in alleles at three high-molecular-weight glutenin (HMW-glu) seed storage protein loci. The 48 RILs were classified by SDS-PAGE for the Anza alleles Glu-Alc (null), Glu-B1b (subunits 7 + 8), and Glu-D1a (subunits 2 + 12) and for Cajeme 71 alleles Glu-A1a (sub-unit 1), Glu-B1I (subunits 17 + 18), and Glu-D1d (subunits 5 + 10). All RILs and parents were grown in a replicated field trial with three levels of nitrogen (N) fertilization. Additive and additive x additive gene effects for the three loci were detected by orthogonal comparisons of means for each of six wheat end-use quality traits. Each HMW-glu genotype was represented by three to ten RILs so that variability among RILs within each HMW-glu genotype could be examined. N effects were consistently small. All traits except flour yield were highly correlated with predictor traits studied earlier. Flour protein content, baking water absorption, dough mixing time, bread loaf volume, and bread loaf crumb score were all correlated, suggesting similar gene control for these traits; however, specific additive locus contributions were evident: αB for flour yield; αB and αD for flour protein; and αB for absorption, but differing in sign; all three loci for mixing time, but αB was negative; and all three loci were positively associated with loaf volume. Digenic epistatic effects were significant for flour yield (αAD), flour protein (αAB), and absorption and mixing time (αAD, αBD). Only flour yield showed a trigenic epistatic effect. Six of seven epistatic effects were negative, thus showing how progress in breeding for high quality may be impeded by interaction of genes which, by themselves, have strong positive additive effects. Considerable genetic variance among RILs within a HMW-glu genotype was detected for all traits, and the summation of α effects accounted for a mean of 13% of the parental differences for the six traits examined in this study. Clearly, further resolution of the genetics of wheat quality would be desirable from a plant breeding point of view.

Breeding for Salinity‐Stressed Environments: Recombinant Inbred Wheat Lines under Saline Irrigation

Disposal of saline drainage water poses a difficulty in some cropping systems. This study investigated the reuse of such water for irrigating winter‐planted spring wheat (Triticum aestivum L.) in the San Joaquin Valley of California. Uniform salinization with a controlled degree of salinity presents a new target cropping system for plant breeding. Our objectives were to measure genetic and environmental variance components for agronomic traits and stress susceptibility index (S), using 43 recombinant inbred lines (RILs) and their parents, ‘Anza’ and ‘Cajeme 71’, grown under three saline irrigation treatments (control, 0.6; intermediate, 7.0; and high, 14.0 dS m‐1) and two N fertilization rates (160 and 260 kg N ha‐1) in 2 yr. Soil water conductivities at harvest time were 1.2, 4.4, and 9.4 dS m‐1 (2 yr means) after the three irrigation treatments. Grain yield reductions after the 7.0 and 14.0 dS m‐1 treatments were 5 and 19% in the first year and 36 and 68% in the second year. In both years genetic variances were significant and genotype ✕ environment interaction variances were not significant for grain and biomass yields and harvest index. Broad‐sense heritabilities estimated each year were low for grain yield (0.30 and 0.10) and biomass (0.07 and 0.02). Differences in S, based on grain yields in the low and intermediate salinity treatments, were nonsignificant in both years among RIL, but indicated a higher salinity tolerance of Anza than Cajeme 71. It was suggested that selection in low salinity environments would produce cultivars with high yield potential for environments with moderate salinity stress (soil conductivity of ≈7 dS m‐1), as may be prescribed with a controlled saline irrigation cropping system for wheat.

Use of recombinant inbred lines of wheat for study of associations of high-molecular-weight glutenin subunit alleles to quantitative traits

The high-molecular-weight glutenin subunits (HMW glutenin), encoded by alleles at homoeologous lociGlu-A1,Glu-B1, andGlu-D1 on the long arms of chromosomes1A,1B, and1D of a set of F8 random recombinant inbred lines (RIL) derived from the bread wheat cross Anza × Cajeme 71, were classified by SDS-PAGE. Anza has poor breadmaking quality and HMW-glutenin subunits (Payne numbers) null (Glu-A1c), 7+8 (Glu-B1b), and 2+12 (Glu-D1a); Cajeme 71 has good quality and 1 (Glu-A1a), 17+18 (Glu-B1i), and 5+10 (Glu-D1d). The combinations of these alleles in the RIL were examined for associations with grain yield and four indicators of grain quality - protein content, yellowberry, pearling index, and SDS sedimentation volume. Data were obtained from a field experiment with three nitrogen fertilization treatments on 48 RIL and the parents. Orthogonal partitioning of the genetic variance associated with the three HMW glutenin subunit loci into additive and epistatic (digenic and trigenic) effects showed strong associations of these loci with grain yield and the indicators of quality; however, the associations accounted for no more than 25% of the differences between the parents. Genetic variance was detected among the RIL, which had the same HMW glutenin genotype for all traits. Epistatic effects were absent for grain yield and yellowberry, but were substantial for grain protein content, pearling index, and SDS sedimentation volume. All three loci had large single-locus additive effects for grain yield, protein, and SDS sedimentation volume. Yellowberry was largely influenced byGlu-B1 andGlu-D1, whereas pearling index was associated withGlu-A1 andGlu-B1. Even though the observed associations-of effects of HMW glutenin loci with the quantitative characters were small relative to the total genetic variability, they are of considerable importance in understanding the genetics of wheat quality, and are useful in the development of new wheat varieties with specific desired characteristics.