Genetic characterisation of dough rheological properties in a wheat doubled haploid population: additive genetic effects and epistatic interactions

Detection of quantitative trait loci for heading date based on the doubled haploid progeny of two elite Chinese wheat cultivars

Quantitative trait loci (QTLs) with epistatic and QTL x environment (QE) interaction for heading date were studied using a doubled haploid (DH) population containing 168 progeny lines derived from a cross between two elite Chinese wheat cultivars Huapei 3 x Yumai 57 (Triticum aestivum L.). A genetic map was constructed based on 305 marker loci, consisting of 283 SSR loci and 22 EST-SSR markers, which covered a total length of 2141.7 cM with an average distance of 7.02 cM between adjacent markers in the genome. QTL analyses were performed using a mixed linear model approach. Two main-effect QTLs and two pairs of digenic epistatic effects were detected for heading date on chromosomes 1B, 2B, 5D, 6D, 7A, and 7D at three different environments in 2005 and 2006 cropping seasons. A highly significant QTL with an F-value 148.96, designated as Qhd5D, was observed within the Xbarc320-Xwmc215 interval on chromosome 5DL, accounting for 53.19% of the phenotypic variance and reducing days-to-heading by 2.77 days. The Qhd5D closely links with a PCR marker Xwmc215 with the genetic distance 2.1 cM, which can be used in molecular marker-assisted selection (MAS) in wheat breeding programs. Moreover, the Qhd5D was located on the similar position of well-characterised vernalization sensitivity gene Vrn-D1. We are also spending more efforts to develop near-isogenic lines to finely map the Qhd5D and clone the gene Vrn-D1 through map-based cloning. The Qhd1B with additive effect on heading date has not been reported in previous linkage mapping studies, which might be a photoperiod-sensitive gene homoeologous to the Ppd-H2 gene on chromosome 1B. No main-effect QTLs for heading date were involved in epistatic effects.

Novel x-type high-molecular-weight glutenin genes from Aegilops tauschii and their implications on the wheat origin and evolution mechanism of Glu-D1-1 proteins

Two new x-type high-molecular-weight glutenin subunits with similar size to 1Dx5, designated 1Dx5*t and 1Dx5.1*t in Aegilops tauschii, were identified by SDS-PAGE, RP-HPLC, and MALDI-TOF-MS. The coding sequences were isolated by AS-PCR and the complete ORFs were obtained. Allele 1Dx5*t consists of 2481 bp encoding a mature protein of 827 residues with deduced Mr of 85,782 Da whereas 1Dx5.1*t comprises 2526 bp encoding 842 residues with Mr of 87,663 Da. The deduced Mr's of both genes were consistent with those determined by MALDI-TOF-MS. Molecular structure analysis showed that the repeat motifs of 1Dx5*t were correspondingly closer to the consensus compared to 1Dx5.1*t and 1Dx5 subunits. A total of 11 SNPs (3 in 1Dx5*t and 8 in 1Dx5.1*t) and two indels in 1Dx5*t were identified, among which 8 SNPs were due to C-T or A-G transitions (an average of 73%). Expression of the cloned ORFs and N-terminal sequencing confirmed the authenticities of the two genes. Interestingly, several hybrid clones of 1Dx5*t expressed a slightly smaller protein relative to the authentic subunit present in seed proteins; this was confirmed to result from a deletion of 180 bp through illegitimate recombination as well as an in-frame stop codon. Network analysis demonstrated that 1Dx5*t, 1Dx2t, 1Dx1.6t, and 1Dx2.2* represent a root within a network and correspond to the common ancestors of the other Glu-D-1-1 alleles in an associated star-like phylogeny, suggesting that there were at least four independent origins of hexaploid wheat. In addition to unequal homologous recombination, duplication and deletion of large fragments occurring in Glu-D-1-1 alleles were attributed to illegitimate recombination.

Genetic analysis of bread-making quality scores in bread wheat using a recombinant inbred line population

Bread-making quality has been evaluated in a progeny of 194 recombinant inbred lines (RILs) from the cross between the two French cultivars Récital and Renan, cultivated in three environments. These cultivars have been previously identified as having contrasting grain protein content and dough rheology properties, although they achieve similar scores for the official bread-making test used for cultivar registration in France. However the progeny displayed a wide range of variations, suggesting that favourable alleles at several loci are present in the two parental lines. Correlation analyses revealed that bread-making scores are poorly correlated among environments, as they are poorly predicted by multiple regression on dough rheology parameters and flour-protein content. However, loaf volume was the most heritable and predictable trait. A total of seven QTLs were found for bread scores, each explaining 5.9-14.6% of trait variation and six for the loaf volume (10.7-17.2%). Most bread-making QTLs, and particularly those detected in all environments, co-located with QTLs for dough rheology, protein content or flour viscosity due to soluble pentosans (Fincher and Stone 1986; Anderson et al. in J Cereal Sci 19:77-82, 1994). Some QTL regions such as those on chromosome 3A and chromosome 7A, which display stable QTLs for bread-making scores and loaf volume, were not previously known to host obvious genes for grain quality.

Novel DNA variations to characterize low molecular weight glutenin Glu-D3 genes and develop STS markers in common wheat

Low-molecular-weight glutenin subunits (LMW-GS) play an important role in bread and noodle processing quality by influencing the viscoelasticity and extensibility of dough. The objectives of this study were to characterize Glu-D3 subunit coding genes and to develop molecular markers for identifying Glu-D3 gene haplotypes. Gene specific primer sets were designed to amplify eight wheat cultivars containing Glu-D3a, b, c, d and e alleles, defined traditionally by protein electrophoretic mobility. Three novel Glu-D3 DNA sequences, designated as GluD3-4, GluD3-5 and GluD3-6, were amplified from the eight wheat cultivars. GluD3-4 showed three allelic variants or haplotypes at the DNA level in the eight cultivars, which were designated as GluD3-41, GluD3-42 and GluD3-43. Compared with GluD3-42, a single nucleotide polymorphism (SNP) was detected for GluD3-43 in the coding region, resulting in a pseudo-gene with a nonsense mutation at the 119th position of deduced peptide, and a 3-bp insertion was found in the coding region of GluD3-41, leading to a glutamine insertion at the 249th position of its deduced protein. The coding regions for GluD3-5 and GluD3-6 showed no allelic variation in the eight cultivars tested, indicating that they were relatively conservative in common wheat. Based on the 12 allelic variants of three Glu-D3 genes identified in this study and three detected previously, seven STS markers were established to amplify the corresponding gene sequences in wheat cultivars containing five Glu-D3 alleles (a, b, c, d and e). The seven primer sets M2F12/M2R12, M2F2/M2R2, M2F3/M2R3, M3F1/M3R1, M3F2/M3R2, M4F1/M4R1 and M4F3/M4R3 were specific to the allelic variants GluD3-21/22, GluD3-22, GluD3-23, GluD3-31, GluD3-32, GluD3-41 and GluD3-43, respectively, which were validated by amplifying 20 Chinese wheat cultivars containing alleles a, b, c and f based on protein electrophoretic mobility. These markers will be useful to identify the Glu-D3 gene haplotypes in wheat breeding programs.

Matrix-assisted laser desorption/ionization time-of-flight based wheat gliadin protein peaks are useful molecular markers for wheat genetic study

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instrumentation has been used to analyze wheat seed gliadins as an alternative to other established methods, including sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), capillary electrophoresis (CE), high-performance liquid chromatography (HPLC), etc. The MALDI-TOF approach has shown to have many advantages such as high resolution, cost effectiveness and high throughput. MALDI-TOF-based gliadin profiles have been used for fast wheat cultivar identification. However, the genetic information represented by individual gliadin peaks has not been utilized. In this study a wheat doubled haploid population with a genetic linkage map of good coverage was used to assay individual gliadin peaks from MALDI-TOF profiles as molecular markers. Eight segregating peaks in the population were scored as polymorphic across the population. The 1 to 1 segregating ratios validated the scoring of the peaks and all peaks were mapped to the expected chromosomes or linkage groups on the available linkage map: 1 peak on chromosome 1A, 1 on 6A, 4 on 6B and 2 on 6D.

Characterization of three low-molecular-weight Glu-D3 subunit genes in common wheat

Low-molecular-weight glutenins (LMW-GS) in common wheat (Triticum aestivum L.) are of great importance for processing quality of pan bread and noodles. The objectives of this study are to identify LMW-GS coding genes at GluD3 locus on chromosome 1D and to establish relationships between these genes and GluD3 alleles (a, b, c, d, and e) defined by protein electrophoretic mobility. Specific primer sets were designed to amplify each of the three LMW-GS chromosome 1D gene regions including upstream, coding and downstream regions of eight wheat cultivars containing GluD3 a, b, c, d and e alleles. Three LMW-GS genes, designated as GluD3-1, GluD3-2 and GluD3-3, were amplified from the eight wheat cultivars. The allelic variants of these three genes were analysed at the DNA and protein level. GluD3-1 showed two allelic variants or haplotypes, one common to cultivars containing protein alleles a, d and e (designated GluD3-11) and the other was present in cultivars with alleles b and c (designated GluD3-12). Comparing with GluD3-12, a 3-bp deletion was found in the coding region of the N-terminal repetitive domain of GluD3-11, leading to a glutamine deletion at the 116th position. GluD3-2 had three variants at the DNA level in the eight cultivars, which were designated as GluD3-21, GluD3-22 and GluD3-23. In comparison to GluD3-21, a single nucleotide polymorphism (SNP) was detected for GluD3-22 in the signal peptide region, resulting in an amino acid change from alanine to threonine at the 11th position; and 11 mutations were found at GluD3-23, with five in upstream region, four in coding region and two in downstream region, respectively. GluD3-3 had two haplotypes, designated as GluD3-31 and GluD3-32, both belonging to LMW-s glutenin subunits though their first amino acids in N-terminal region are different. Compared with the GenBank GluD3 genes, nucleotide sequences of GluD3-21 and GluD3-23 were the same as X13306 and AB062875, respectively. GluD3-22 and GluD3-11 had only one-base difference from U86027 and AB062865. GluD3-12 was not found in the GenBank database, indicating a newly identified GluD3 gene variation. GluD3-3 was a new gene different from any other known GluD3 genes. Analyses of the relationship between Glu-D3 alleles defined by protein electrophoretic mobility and different GluD3 gene variations at the DNA or protein level provided molecular basis for DNA based identification of glutenin alleles.

The PDI genes of wheat and their syntenic relationship to the esp2 locus of rice

The storage protein polymers in the endosperm, stabilised by disulphide bonds, determine a number of processing qualities of wheat dough. The enzyme protein disulphide isomerase (PDI), involved in the formation of disulphide bonds, is strongly suggested to play a role in the formation of wheat storage protein bodies. Reports of the rice mutant esp2 exhibiting aberrant storage protein deposition in conjunction with a lack of PDI expression provided strong indications of a direct role for PDI in storage protein deposition. The potential significance of wheat PDI prompted the present studies into exploring any orthology between wheat PDI genes and rice PDI and esp2 loci. By designing allele-specific (AS)-polymerase chain reaction (PCR) markers, two of the three wheat PDI genes could be genetically mapped to group 4 chromosomes and showed close association with GERMIN genes. Physical mapping led to localisation of wheat PDI genes to chromosomal "bins" on the proximal section of chromosome 4AL and distal sections of 4BS and 4DS. Identification of the putative PDI gene of rice and its comparison to the esp2 locus revealed that they were present at similar positions on the short arm of chromosome 11. Analysis of a large section of the PDI-containing section of rice chromosome 11S revealed a number of putative orthologues from The Institute for Genomic Research Triticum aestivum Gene Index database, of which five had been mapped, each localising to group 4 chromosomes, many in good agreement with our mapping results. The results strongly suggest a close linkage between the esp2 marker and the PDI gene of rice and an orthology between the PDI loci of rice and wheat and predict quantitative-trait loci involved in storage protein deposition at the PDI loci.