Genetic diversity and association mapping of agronomic yield traits in eighty six synthetic hexaploid wheat

Association mapping is a method to identify associations between target traits and genetic markers based on linkage disequilibrium (LD) of a quantitative trait locus. Synthetic hexaploid wheat (SHW) is derived from a cross between Triticum durum Desf. and Aegilops tauschii Coss. that enhances genetic diversity and broadens breeding resources. In this study, phenotypic diversity in 110 wheat accessions (86 SHW germplasm specimens and 24 conventional wheat varieties) was evaluated quantitatively for yield characteristics of grains per spike, thousand kernel weight, and spike length. Phenotypic data were collected over two years at two locations, and 1785 alleles were detected (mean 6.59), ranging from 3 to 11 alleles per locus. The average genetic diversity index was 0.749, with a range from 0.239 to 0.923. The polymorphic information content (PIC) ranged from 0.145 to 0.968, with a mean value of 0.695. The genetic diversity index and PIC indicated that genome B > D > A. Accessions were grouped into three subgroups based on STRUCTURE and unweighted pair-group with arithmetic mean clustering. The mean LD decay across the genome was 11.78 cM. Association mapping between traits and simple sequence repeat markers was performed using the generalized linear model approach. Forty-six SSR loci were significantly associated with the measured agronomic traits in two geographic locations. Together, these results broaden our knowledge of how to harness elite genes and genetic diversity in SHW in genomic and marker-assisted selection.     

The low down on association mapping in hexaploid wheat (Triticum aestivum L.)

The past few decades have witnessed hundreds of family-based linkage studies mapping for numerous traits but only a limited number of QTLs were actually cloned, tagged, or used for marker-assisted selection. Although providing valuable information, this conventional approach cannot be scaled up to underpin the incredible amount of phenotypic variation in the form of 266, 589 hexaploid wheat accessions maintained in public germplasm collections. Association mapping has recently emerged as an alternative and more powerful mapping approach where a natural population is surveyed to determine marker-trait associations using linkage disequilibrium (LD). After its first application for milling quality in 2006, association mapping studies in hexaploid wheat are being extended to tag yield traits, protein quality, and tolerance to biotic and abiotic stresses. Advances in genotyping technology and statistical approaches greatly accelerated the shift from conventional linkage-based mapping to LD-based association mapping. Association mapping stands out because of simultaneous utilization of a large number of ex situ-conserved natural variation due to historical recombination events accumulated over centuries.     

Genetic mapping within the wheat D genome reveals QTL for germination, seed vigour and longevity, and early seedling growth

Quantitative trait loci (QTL) controlling germination, seed vigour and longevity, and early seedling growth were identified using a set of common wheat lines carrying known D genome introgression segments. Seed germination (capacity, timing, rate and synchronicity) was characterized by a standard germination test, based either on the 1 mm root protrusion (germination sensu stricto) or the development of normal seedlings. To quantify seed vigour, the same traits were measured from batches of seed exposed for 72 h at 43°C and high (ca. 100%) humidity. Seed longevity was evaluated from the relative trait values. Seedling growth was assessed both under non-stressed and under osmotic stress conditions. Twenty QTL were mapped to chromosomes 1D, 2D, 4D, 5D, and 7D. Most of the QTL for germination sensu stricto clustered on chromosome 1DS in the region Xgwm1291–Xgwm337. A region on chromosome 7DS associated with Xgwm1002 harboured loci controlling the development of normal seedlings. Seed vigour-related QTL were present in a region of chromosome 5DL linked to Xgwm960. QTL for seed longevity were coincident with those for germination or seed vigour on chromosomes 1D or 5D. QTL for seedling growth were identified on chromosomes 4D and 5D. A candidate homologues search suggested the putative functions of the genes within the respective regions. These results offer perspectives for the selection of favourable alleles to improve certain vigour traits in wheat, although the negative effects of the same chromosome regions on other traits may limit their practical use.     

Genetic control of esterase-6 isozymes in hexaploid wheat and rye

Summary The EST-6 leaf esterase phenotypes from euploid, nullisomic-tetrasomic and rye chromosome addition and substitution lines of common wheat were determined using polyacrylamide gel electrophoresis. Evidence is presented to demonstrate that Est-6 is a new set of genes, that are expressed in the leaf. The Est-6 gene set were clearly distinguished from the Est-5 genes which are expressed in the grain. The three homoeoallelic loci, Est-A6, Est-B6 and Est-D6, were located on chromosomes 3A, 3B and 3D. An Est-R6 gene was located on chromosome 6R is involved in rye. Some considerations concerning homoeology between homoeologous group 3 of wheat and the rye chromosome 6R are made.     

Genome-wide association study reveals loci associated with seed longevity in common wheat (Triticum aestivum L.)

Seed longevity could significantly determine seed regeneration cycle and greatly affect wheat production. With the 90 K chip assays, a genome-wide association study was performed to identify seed longevity-related markers and loci in common wheat. Seed germination ratios (GR) under artificially ageing of 166 wheat accessions across three environments were evaluated to assess seed longevity. Totally, 23 longevity-related loci were identified in the study, explaining 6.7%–11.4% of the phenotypic variations. Of these, QlgGR.cas-1A and QlgGR.cas-2B.2 were deemed as stable loci associated with wheat seed longevity. Fifteen loci were found overlapped with known quantitative trait loci or genes. Besides, QlgGR.cas-1A, QlgGR.cas-2B.2, QlgGR.cas-3D.1, QlgGR.cas-3D.2, QlgGR.cas-4A.2, QlgGR.cas-5A.1, QlgGR.cas-5A.2 and QlgGR.cas-6A.1 were colocated with seed dormancy-related loci. Significant additive effects were obtained for seed longevity by pyramiding favourable alleles. Several candidate genes were found involved in signal transduction and stress resistance pathways by sequencing analysis of significantly longevity-related molecular markers. These results might provide new sights into the genetic architecture of seed longevity.     

Identifying AFLP and microsatellite markers for vernalization response gene Vrn-B1 in hexaploid wheat using reciprocal mapping populations

Marker‐assisted selection may be useful for combining specific vernalization response (Vrn) alleles into a single wheat genotype for yield enhancement; however, DNA markers are only available for two of the three genes identified to date. The objectives of this study were to investigate reciprocal effects on days to heading using F₂ populations generated by cross‐hybridizing near‐isogenic lines (NILs) carrying spring (Vrn‐B1; TDB) and winter (vrn‐B1; TDC) alleles, and to identify markers linked to Vrn‐B1 through genetic linkage analysis. Heading data were recorded for 91 and 89 progeny from reciprocal mapping populations TDB/TDC and TDC/TDB, respectively, and significant (P < 0.0001) reciprocal and dominance effects were detected. Among 207 amplified fragment length polymorphisms primer pairs and seven wheat microsatellite markers screened, two and one, respectively, were linked distally to Vrn‐B1 on wheat chromosome 5BL. Microsatellite Xgwm408 was most closely linked to Vrn‐B1 at 3.9 and 1.1 cM in the TDB/TDC and TDC/TDB map, respectively. Reciprocal differences in recombination distances emphasize the importance of female parent choice when generating mapping populations. Molecular markers are now available for three Vrn loci in wheat.     

Genetic analysis of hexaploid wheat,Triticum aestivum using intervarietal chromosome substitution lines—protein content and grain weight

Summary The 21 intervarietal chromosome substitution lines of the cultivar Hope in Chinese Spring were used to analyse the genetic differences between the two cultivars Hope and Chinese Spring in grain protein content and grain weight.Only one chromosome of Hope, 5D, significantly influenced grain protein content of Chinese Spring. Its influence was of only minor effect and was to decrease protein content expression of Chinese Spring. It has been postulated that the genetic control of protein content, in this instance, is most likely due to many genes each of small effect.Five chromosomes of Hope influenced the 1000 grain weight value of normal Chinese Spring, all increasing its expression. Chromosomes 1A, 4A and 5B were of major effect and 3A and 6A of comparatively minor effect. A minimal estimate of five genes determines the difference in grain size between these cultivars. The possible evolutionary significance of the contribution of the A genome of bread wheat to grain size determination is discussed. On the basis of certain findings of this study, proposals are made for breeding for increased grain size in hexaploid wheat.     

Advantages of seed selection in wheat aneuploid studies

Summary Aneuploid studies in wheat often involve progenies which segregate for monosomics and disomics. In situations where only monosomics are needed, data are presented to show that their frequency can be increased by selecting wrinkled seeds for planting. Conversely, a higher proportion of disomics results from using the plumpest seeds from a cross- or self-pollination involving a monosomic parent.Published with the approval of the Director as Paper No. 2712, Journal Series, Nebraska Agric. Expt. Station.     

Genetic diversity of high-molecular-weight glutenin subunit compositions in landraces of hexaploid wheat from Japan

The high-molecular-weight (HMW) glutenin subunit composition of seed storage protein of 174 Japanese hexaploid wheat (Triticum aestivum) landraces have been examined by using sodium dodecyl sulfate polyacrylamide gel electrophoresis system. Twenty four different, major glutenin HMW subunits were identified, and each of the landraces contained three to five subunits and 17 different glutenin subunit patterns were observed for 13 alleles in the landraces. On the basis of HMW glutenin subunits composition, Japanese landraces showed a specific allelic variation, close to Japanese commercial wheats in HMW glutenin subunits, different from those in alien hexaploid wheats. Further, it could be concluded that all common glutenin alleles can be found in the 174 landraces originated from Japan. The variation detected in the glutenin subunits is useful for variety identification, has a bearing on our understanding of hexaploid wheat genetic resource evolution in Japan, and raises questions concerning the nature of this genetic variation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Production of polyhaploids of hexaploid wheat using stored pearl millet pollen

The effects of drying and freezing on viability of pearl millet pollen were examined with the aim of using stored pollen in polyhaploid production of hexaploid wheat. Freshly collected pollen of pearl millet line NEC 7006 with 55% water content, germinated at a frequency of 80%. Pollen that was dried for two hours to 6% water content showed 50% germination frequency and maintained similar frequencies after the freezing process. In crosses of hexaploid wheat variety Norin 61 with fresh pearl millet pollen, embryos were obtained at a frequency of 27.6%. In crosses with pollen stored at -196 °C, -80 °C and -20 °C for one month, embryo formation frequencies ranged from 27.5 to 17.4%. After five and twelve months of storage, the frequencies ranged from 29.7 to 14.6% at storage temperatures of -196 °C and -80 °C, and from 8.0 to 3.2% at -20 °C, indicating significant differences among storage temperatures. However, no significant frequency difference was found among pollen water contents at the time of collection. All plants regenerated from crosses with pearl millet pollen stored for five months were wheat polyhaploids. These results suggest that stored pearl millet pollen is an efficient medium for producing polyhaploids in hexaploid wheat. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic control of some polymeric glutenin fractions in hexaploid wheat (Triticum aestivum)

Reciprocal crosses were made between seven different hexaploid wheat genotypes. Hybrid kernels and their parents were used to determine the amount of polymeric glutenin fractions by size-exclusion high-performance liquid chromotography (SE-HPLC) analysis. Quantitative aspects of the genetic control for various glutenin fractions were investigated through diallel cross analysis. The association between the potential effect on hexaploid wheat quality of various allelic types and the quantitative expression of the polymeric glutenin fractions was confirmed. Significant average heterosis effects were demonstrated for insoluble glutenin (pFi), total soluble and insoluble glutenin (pF1 + pF2 + pFi) and the ratio of soluble to insoluble glutenin, (pF1 + pF2)/pFi. Some genotypes showed significant positive or negative combining abilities and general reciprocal effects for the glutenin fractions studied. For gluten quality, ‘Qualital’ was the best combiner for determining an optimal glutenin composition (high values for pFi and pF1 + pF2 + pFi and low values for pF1/pF2 and (pF1 + pF2)/pFi, respectively). These results should be of great interest in breeding programmes aimed at improving hexaploid wheat quality.     

An association mapping analysis of dormancy and pre-harvest sprouting in wheat

Seed dormancy and pre-harvest sprouting are important traits in bread wheat. Bi-parental populations have permitted the identification of several genes/quantitative trait loci controlling these traits, mapping to various bread wheat chromosomes. Here, we report the use of association mapping to uncover the genetic basis of both traits in a panel of 96 diverse winter wheat cultivars to establish the presence of marker-trait associations on many chromosomes. Potential candidate genes were identified by studying the gene content of the chromosome bins into which the major marker trait associations mapped.     

Genome-wide association study reveals favorable alleles associated with common bunt resistance in synthetic hexaploid wheat

Genetic resistance to common bunt is a cost-effective, environmentally friendly, and sustainable approach to controlling the disease. To date, 16 race specific common bunt resistance genes (Bt1-Bt15 and Btp) have been reported in wheat. However, a limited number have been mapped and few markers have been identified, which limits the usage of molecular markers in a marker-assisted breeding program. A total of 125 synthetic hexaploid wheats (SHWs) were evaluated for reactions to a mixture of common bunt races under field conditions in Turkey in 2016 and 2017. The objectives of this study were to identify common bunt resistant genotypes, identify genomic regions conferring resistance to common bunt using 35,798 genotyping-by-sequencing derived single nucleotide polymorphisms (SNPs), and investigate the significant SNPs present within genes using the functional annotations of the underlying genes. We found 29 resistant SHWs that can be used in wheat breeding. The genome-wide association study identified 15 SNPs associated with common bunt resistance and a haplotype block comprising three SNPs in perfect linkage disequilibrium. Five of them were novel and were located on chromosomes 2A, 3D, and 4A. Furthermore, seven of the 15 SNPs were found within genes and had annotations suggesting potential role in disease resistance. This study identified several favorable alleles that decreased common bunt incidence up to 26% in SHWs. These resistant SHWs and candidate genomic regions controlling common bunt resistance will be useful for wheat genetic improvement and could assist in further understanding of the genetic architecture of common bunt resistance.     

Genetic mapping of sedimentation volume across environments using recombinant inbred lines of durum wheat

SDS-sedimentation volume (SV) is a biochemical index widely used to evaluate flour quality in durum and bread wheats. Significant association between SV and endosperm proteins (gliadin, high-molecular-weight- and low-molecular-weight-glutenin subunits) have been reported. Protein loci, however, account for only a portion of the total genetic variability. The objective of this study was to identify and locate quantitative trait loci (QTLs) associated with SV in a set of recombinant inbred (RI) lines, derived from a cross between the cv.‘Messapia’ of durum wheat and the accession MG4343 of the var. dicoccoides, and characterized for 259 genetic and molecular (RFLP) markers. Significant differences were detected for the quality index in the six environments examined, while the pattern of variability was that of a quantitative trait. Regression analysis of marker loci and sedimentation volume indicated, as expected, that chromosome 1B, on which are located the Gli-B 1/Glu-B 3 loci for some gliadin and glutenin subunits, is important for wheat quality. Two additional regions located on chromosomes 6AL and 7BS, and four regions on 1AL, 3AS, 3BL and 5AL, were shown to have single-factor effects on sedimentation volume at P < 0.001 and P < 0.01, respectively. Positive effects were contributed by both parents. A multiple linear regression model consisting of seven significant loci on different chromosomes explained 62–91% of the genotypic variation of the trait. The availability of linked markers to QTLs may facilitate the genetic dissection of quantitative traits and the early selection in wheat breeding programmes.     

Genetic analysis of seedling resistance to Stagonospora nodorum blotch in selected tetraploid and hexaploid wheat genotypes

Stagonospora nodorum blotch (SNB), caused by Phaeosphaeria nodorum, is a major component of the leaf‐spotting disease complex of wheat (Triticum aestivum L.) in the northern Great Plains of North America. This study was conducted, under controlled environmental conditions, to determine the inheritance of resistance to SNB in a diverse set of hexaploid and tetraploid wheat genotypes and to decipher the genic/allelic relationship among the resistance gene(s). Plants were inoculated at the two to three‐leaf stages with a spore suspension of P. nodorum isolate Kelvington‐SK and disease reaction was assessed 8 days after inoculation based on a lesion‐type scale. Tests of the F₁ and F₂ generations and of F_{2 : 3} or F_{2 : 5} families indicated that a single recessive gene controlled resistance to SNB in both hexaploid and tetraploid resistance sources. Lack of segregation in intra‐specific and inter‐specific crosses between the hexaploid and the tetraploid resistant genotypes, indicated that these genetically diverse sources of resistance possess the same gene for resistance to SNB. Results of this study suggest that the wheat‐P. nodorum interaction may follow the toxin model of the gene‐for‐gene hypothesis.     

小麦生产用种原种化的实践与探索

目前,我国将小麦种子划分为育种家种子、原原种、原种、良种四级.其中,育种家种子和原原种一般都作繁殖材料,而原种既可作为繁育材料,也常用于大田生产;良种则主要用于大田生产,国际上一般称为登记种子或大田用种.