Population structure and long-range linkage disequilibrium in a durum wheat elite collection

A collection of 134 durum wheat accessions, mainly including cultivars (cvs.) representative of the major gene pools, was assembled and characterized with 70 SSRs for genetic diversity and level of long-range linkage disequilibrium (LD). Results of both a distance-based and a model-based (Bayesian) cluster analysis evidenced the presence of a structured diversity. In the model-based analysis, six to eight main distinct subpopulations were identified based on the molecular data. Only a relatively small portion (20%) of the molecular variation was accounted for by the geographical origin of the accessions. Major differences were detected between the North American and the Mediterranean cvs., while a considerable overlap characterized the cvs. from CIMMYT-ICARDA and Italy. The North American cvs. showed the highest within group mean genetic similarity (GS_m = 0.68). French cvs. revealed sizeable similarities with both the North American as well as the Italian and CIMMYT-ICARDA pools. Considering the germplasm as a whole, high levels of LD were found both at locus pairs with an intrachromosomal distance <50 cM as well as at those with distances more than 50 cM and independent (86, 52 and 54% of SSR pairs at p < 0.01, respectively). After re-evaluating LD within each of the three main subgroups identified through the analysis of the germplasm structure, the LD level remained high for tightly to moderately linked locus pairs (<20 cM apart), but was greatly reduced in the loosely linked (more than 50 cM apart) and independent locus pairs. The implications of these findings as to the possibility of using association mapping for gene/QTL discovery in durum wheat are discussed.     

A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping

Background

Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement.

Results

High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology^® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman’s rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r² threshold = 0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments.

Conclusions

The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-873) contains supplementary material, which is available to authorized users.     

Integration of dinucleotide microsatellites from hexaploid bread wheat into a genetic linkage map of durum wheat

 Seventy nine microsatellite markers from hexaploid bread wheat (T. aestivum L.) were integrated into a genetic linkage map of durum wheat (T. turgidum ssp. durum (Desf.) Huns.) created by RFLP segregation data from a population of 65 recombinant inbred lines. The results indicate a relatively even distribution of microsatellite loci and demonstrate that microsatellite markers from hexaploid wheat provide an excellent source of molecular markers for use in the genetics and breeding of durum wheat. Received: 16 July 1998 / Accepted: 13 October 1998     

Genome-wide linkage disequilibrium in two Japanese beef cattle breeds

There is little knowledge about the degree of linkage disequilibrium (LD) in beef cattle. This study aims to perform a genome-wide search for LD in Japanese Black and Japanese Brown beef cattle and to compare the level of LD between these two breeds. Parameter D' (the LD coefficient) was used as a measure of LD, and LD was tested for significance of allelic associations between syntenic and between non-syntenic marker pairs. Effects of breed, chromosome, genetic map distance and their interactions with D' were tested based on least squares analyses. Both breeds showed high levels of LD, which ranged over several tens of cM and declined as the marker distance increased for syntenic marker pairs. A rapid decline of the D' value was observed between markers that were spaced 5 and 20 cM apart. LD was significant in most cases for marker pairs <40 cM apart but was not significant between non-syntenic loci. The pattern of LD found in these two breeds was similar to that previously published for dairy cattle. The D' value between breeds was not significantly different (P > 0.05), but the interaction between breed and chromosome was highly significant (P < 0.001). Genetic selection seems to have caused the heterogeneity of the D' values among chromosomes within breed. These results indicate that LD mapping is a useful tool for fine-mapping quantitative trait loci of economically important traits in Japanese beef cattle.     

A genetic linkage map of durum wheat

 A genetic linkage map of tetraploid wheat [Triticum turgidum (L.) Thell.] was constructed using segregation data from a population of 65 recombinant inbred lines (RILs) derived from a cross between the durum wheat cultivar Messapia and accession MG4343 of T. turgidum (L.) Thell. ssp dicoccoides (Korn.) Thell. A total of 259 loci were analysed, including 244 restriction fragment length polymorphisms (RFLPs), one PCR (polymerase chain reaction) marker (a sequence coding for a LMW (low-molecular-weight) glutenin subunit gene located at the Glu-B3 locus), seven biochemical (six seed-storage protein loci and one isozyme locus) and seven morphological markers. A total of 213 loci were mapped at a LOD≥3 on all 14 chromosomes of the A and B genomes. The total length of the map is 1352 cM and the average distance between adjacent markers is 6.3 cM. Forty six loci could not be mapped at a LOD≥3. A fraction (18.6%) of the markers deviated significantly from the expected Mendelian ratios; clusters of loci showing distorted segregation were found on chromosomes 1B, 3AL, 4AL, 6AL and 7AL. The durum wheat map was compared with the published maps of bread wheat using several common RFLP markers and general features are discussed. The markers detected the known structural rearrangements involving chromosomes 4A, 5A and 7B as well as the translocation between 2B-6B, but not the deletion on 2BS. This map provides a useful tool for analysing and breeding economically important quantitative traits and for marker-assisted selection, as well as for studies of genome organisation in small grain cereal species. Received: 5 January 1998 / Accepted: 31 March 1998     

Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers

Key message

We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay.

Abstract

Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai?×?Shi 4185 (D?×?S), Gaocheng 8901?×?Zhoumai 16 (G?×?Z) and Linmai 2?×?Zhong 892 (L?×?Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5–32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

     

Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers

Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of <5% were found in the landrace and modern variety gene pools, respectively, indicating greater numbers of rare variants, or likely new alleles, in landraces. Analysis of molecular variance (AMOVA) showed that A genome had the largest genetic differentiation and D genome the lowest. In contrast to genetic diversity, modern varieties displayed a wider average LD decay across the whole genome for locus pairs with r(2)>0.05 (P<0.001) than the landraces. Mean LD decay distance for the landraces at the whole genome level was <5 cM, while a higher LD decay distance of 5-10 cM in modern varieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5 ～ 25 cM) compared to landraces (<5 ～ 15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources.     

Null alleles for gliadin blocks in bread and durum wheat cultivars

Summary Wheat gliadin proteins are coded by clusters of genes (complex loci) located on the short arms of chromosomes of homoeologous groups 1 and 6 in bread (6x) and durum (4x) wheats. The proteins expressed by the various complex loci have been designated gliadin blocks. In a survey of accessions from the Germplasm Institute (C.N.R., Bari, Italy) collection, several different accessions have been found that lack particular blocks of proteins (null alleles). In some bread wheat accessions, seeds do not express gliadins that are coded by chromosomes 1D and 6A in normal cultivars. Similarly, some durum wheat accessions lack -gliadin components coded for by genes on chromosomes 1A and 1B. The missing proteins do not result from the absence of whole chromosomes, but may be the consequence of partial deletion of these genes at a complex locus or result from their silencing.     

An integrated DArT-SSR linkage map of durum wheat

Genetic mapping in durum wheat (Triticum durum Desf.) is constrained by its large genome and allopolyploid nature. We developed a Diversity Arrays Technology (DArT) platform for durum wheat to enable efficient and cost-effective mapping and molecular breeding applications. Genomic representations from 56 durum accessions were used to assemble a DArT genotyping microarray. Microsatellite (SSR) and DArT markers were mapped on a durum wheat recombinant inbred population (176 lines). The integrated DArT-SSR map included 554 loci (162 SSRs and 392 DArT markers) and spanned 2022 cM (5 cM/marker on average). The DArT markers from durum wheat were positioned in respect to anchor SSRs and hexaploid wheat DArT markers. DArT markers compared favourably to SSRs to evaluate genetic relationships among the durum panel, with 1315 DArT polymorphisms found across the accessions. Combining DArT and SSR platforms provides an efficient and rapid method of generating linkage maps in durum wheat.     

Phytosiderophore release in bread and durum wheat genotypes differing in zinc efficiency

The effect of the zinc (Zn) nutritional status on the rate of phytosiderophore release was studied in nutrient solution over 20 days in four bread wheat (Triticum aestivum cvs. Kiraç-66, Gerek-79, Aroona and Kirkpinar) and four durum wheat (Triticum durum cvs. BDMM-19, Kunduru-1149, Kiziltan-91 and Durati) genotypes differing in Zn efficiency.Visual Zn deficiency symptoms, such as whitish-brown necrosis on leaves and reduction in plant height appeared first and more severe in Zn-inefficient durum wheat genotypes Kiziltan-91, Durati and Kunduru-1149. Compared to the bread wheat genotypes, all durum wheat genotypes were more sensitive to Zn deficiency. BDMM-19 was the least affected durum wheat genotype. Among the bread wheat genotypes, Kirkpinar was the most sensitive genotype. In all genotypes well supplied with Zn, the rate of phytosiderophore release was very low and did not exceed 1 mol 32 plants^-1 3h^-1, or 0.5 mol g^-1 root dry wt 3h^-1. However, under Zn deficiency, with the onset of visual Zn deficiency symptoms, the release of phytosiderophores was enhanced in bread wheat genotypes up to 7.5 mol 32 plants^-1 3h^-1, or 9 mol g^-1 root dry wt 3h^-1, particularly in Zn-efficient Kiraç-66, Gerek-79 and Aroona. In contrast to bread wheat genotypes, phytosiderophore release in Zn-deficient durum wheat genotypes remained at a very low rate. Among the durum wheat genotypes BDMM-19 had highest rate of phytosiderophore release. HPLC analysis of root exudates showed that 2-deoxymugineic acid (DMA) is the dominating phytosiderophore released from roots of Zn-efficient genotypes. In root extracts concentration of DMA was also much higher in Zn-efficient than in inefficient genotypes. The results demonstrate that enhanced synthesis and release of phytosiderophores at deficient Zn supply is involved in Zn efficiency in wheat genotypes. It is suggested that the expression of Zn efficiency mechanism is causally related to phytosiderophore-mediated enhanced mobilization of Zn from sparingly soluble Zn pools and from adsorption sites, both in the rhizosphere and plants.     

Genome-wide scan for bovine twinning rate QTL using linkage disequilibrium

Twinning is a complex trait with negative impacts on health and reproduction, which cause economic loss in dairy production. Several twinning rate quantitative trait loci (QTL) have been detected in previous studies, but confidence intervals for QTL location are broad and many QTL are unreplicated. To identify genomic regions or genes associated with twinning rate, QTL analysis based on linkage combined with linkage disequilibrium (LLD) and individual marker associations was conducted across the genome using high-throughput single nucleotide polymorphism (SNP) genotypes. A total of 9919 SNP markers were genotyped with 200 sires and sons in 19 half-sib North American Holstein dairy cattle families. After SNPs were genotyped, informative markers were selected for genome-wide association tests and QTL searches. Evidence for twinning rate QTL was found throughout the genome. Thirteen markers significantly associated with twinning rate were detected on chromosomes 2, 5 and 14 ( P  < 2.3 × 10⁻⁵). Twenty-six regions on fourteen chromosomes were identified by LLD analysis at P  < 0.0007. Seven previously reported ovulation or twinning rate QTL were supported by results of single marker association or LLD analyses. Single marker association analysis and LLD mapping were complementary tools for the identification of putative QTL in this genome scan.     

Uptake of zinc by rye,bread wheat and durum wheat cultivars differing in zinc efficiency

Effect of zinc (Zn) nutritional status on uptake of inorganic ⁶⁵Zn was studied in rye (Secale cereale, cv. Aslim), three bread wheat (Triticum aestivum, cvs. Dagdas, Bezostaja, BDME-10) and durum wheat (Triticum durum, cv. Kunduru-1149) cultivars grown for 13 days in nutrient solution under controlled environmental conditions. The cultivars were selected based on their response to Zn deficiency and to Zn fertilization in calcareous soils under field conditions. When grown in Zn-deficient calcareous soil in the field, the rye cultivar had the highest, and the durum wheat the lowest Zn efficiency. Among the bread wheats, BDME-10 showed higher susceptibility to Zn deficiency and Bezostaja and Dagdas were less affected by Zn deficiency. Similarly to field conditions, in nutrient solution visual Zn deficiency symptoms (i.e. necrotic lesions on leaf blade) appeared to be more severe in Kunduru-1149 and BDME-10 and less severe in rye cultivar Aslim. Under Zn deficiency, shoot concentrations of Zn were similar between all cultivars. Cultivars with adequate Zn supply did not differ in uptake and root-to-shoot translocation rate of ⁶⁵Zn, but under Zn deficiency there were distinct differences; rye showed the highest rate of Zn uptake and the durum wheat the lowest. In the case of bread wheat cultivars, ⁶⁵Zn uptake rate was about the same and not related to their differential Zn efficiency. Under Zn deficiency, rye had the highest rate of root-to-shoot translocation of ⁶⁵Zn, while all bread and durum wheat cultivars were similar in their capacity to translocate ⁶⁵Zn from roots to shoots. When Zn²⁺ activity in uptake solution ranged between 117 p M and 34550 pM, Zn-efficient and Zn-inefficient bread wheat genotypes were again similar in uptake and root-to-shoot translocation rate of ⁶⁵Zn. The results indicate that high Zn efficiency of rye can be attributed to its greater Zn uptake capacity from soils. The inability of the durum wheat cultivar Kunduru-1149 to have a high Zn uptake capacity seems to be an important reason for its Zn inefficiency. Differential Zn efficiency between the bread wheat cultivars used in this study is not related to their capacity to take up inorganic Zn. This revised version was published online in June 2006 with corrections to the Cover Date.     

Transport interactions between cadmium and zinc in roots of bread and durum wheat seedlings

Field studies have shown that the addition of Zn to Cd-containing soils can help reduce accumulation of Cd in crop plants. To understand the mechanisms involved, this study used ¹⁰⁹Cd and ⁶⁵Zn to examine the transport interactions of Zn and Cd at the root cell plasma membrane of bread wheat ( Triticum aestivum L.) and durum wheat ( Triticum turgidum L. var. durum ). Results showed that Cd²⁺ uptake was inhibited by Zn²⁺ and Zn²⁺ uptake was inhibited by Cd²⁺. Concentration-dependent uptake of both Cd²⁺ and Zn²⁺ consisted of a combination of linear binding by cell walls and saturable, Michaelis-Menten influx across the plasma membrane. Saturable influx data from experiments with and without 10 µm concentrations of the corresponding inhibiting ion were converted to double reciprocal plots. The results revealed a competitive interaction between Cd²⁺ and Zn²⁺, confirming that Cd²⁺ and Zn²⁺ share a common transport system at the root cell plasma membrane in both bread and durum wheat. The study suggests that breeding or agronomic strategies that aim to decrease Cd uptake or increase Zn uptake must take into account the potential accompanying change in transport of the competing ion.     

Inferences about linkage disequilibrium.

Existing theory for inferences about linkage disequilibrium is restricted to a measure defined on gametic frequencies. Unless gametic frequencies are directly observable, they are inferred from genotypic frequencies under the assumption of random union of gametes. Primary emphasis in this paper is given to genotypic data, and disequilibrium coefficients are defined for all subsets of two or more of the four genes, two at each of two loci, carried by an individual. Linkage disequilibrium coefficients are defined for genes within and between gametes, and methods of estimating and testing these coefficients are given for gametic data. For genotypic data, when coupling and repulsion double heterozygotes cannot be distinguished. Burrows' composite measure of linkage disequilibrium is discussed. In particular, the estimate for this measure and hypothesis tests based on it are compared to the usual maximum likelihood estimate of gametic linkage disequilibrium, and corresponding likelihood ratio or contingency chi-square tests. General use of the composite measure, whether or not random union of gametes is an appropriate assumption, is recommended. Attention is given to small samples, where the non-normality of gene frequencies will have greatest effect on methods of inference based on normal theory. Even tools such as Fisher's z-transformation for the correlation of gene frequencies are found to perform quite satisfactorily.     

PCR analysis of x- and y-type genes present at the complex Glu-A1 locus in durum and bread wheat

Genes (x-type) corresponding to different high-molecular-weight glutenin subunits encoded at the Glu-A1 locus present in bread- and durum-wheat cultivars have been selectively amplified by the polymerase chain reaction (PCR). DNA fragments corresponding to an unexpressed x-type gene were also amplified. As unexpressed y-type genes may or may not contain an 8-kb transposon-like insertion, two different sets of primers were designed to obtain amplification of DNA fragments corresponding to these genes. Amplified DNA fragments were also digested with restriction enzymes. The digestion patterns of amplified fragments corresponding to unusual x-type subunits showed similarities with genes encoding the most common subunits 2^* and 1. The unexpressed amplified x-type gene showed a restriction pattern similar to the one obtained with the allelic gene encoding high-molecular-weight glutenin subunit 1; homologies were also found within the repetitive region of the linked y-type genes. On the basis of these observations it is postulated that an ancestral active x-type gene, most likely corresponding to subunit 1, was silenced following the insertion of the 8-kb transposon-like fragment into the linked y-type gene. Received: 8 April 1996 / Accepted: 30 August 1996     

Investigation of the salt tolerance of new Polish bread and durum wheat cultivars

In some regions of the world, low annual precipitation necessitates irrigation of crop plants which usually leads to soil salinity. Due to climatic changes this effect is also expected in the countries of Central Europe, and so in Poland. The aim of the study was (1) to compare tolerance to salt stress of Polish Triticum aestivum cvs. ‘Bogatka’ and ‘Banderola’ with T. durum cv. ‘Komnata’ and breeding line 121, and (2) to indicate the physiological parameter/parameters most suitable for such comparison. The investigation was performed in two experiments. In the first one, the germination ability of caryopses and coleoptiles’ growth were estimated at 0–250 mM of NaCl. The second experiment was conducted on plants grown in a glasshouse in saline soil at 0–150 mM of NaCl for 6 weeks. Salt tolerance was evaluated on the basis of following parameters: chlorophyll fluorescence, net photosynthesis rate (P _N), transpiration rate (E), stomatal conductance (g _s), cell membrane permeability (EL), proline content, fresh weight (FW), dry weight (DW), and relative water content (RWC). Highest germination of caryopses of durum cultivars was recorded at all the salinity levels; however, their coleoptiles were shorter than coleoptiles of bread wheat cultivars. Analysis of chlorophyll fluorescence showed that applied salt doses did not disturb the light phase of photosynthesis in all cultivars under study. Plants of durum wheat showed the higher dissipation of energy excess at the level of the antenna chlorophyll (DIo/CSm) under salinity as compared to plants of bread wheat. Both ‘Komnata’ and line 121 showed stronger P _N reduction as an effect of salinity. A decline of P _N was closely connected with a decrease in g _s. The P _N correlated with a decrease in DW in all studied cultivars except ‘Bogatka’. Control plants of ‘Komnata’ and line 121 were characterized by higher EL and proline level than bread wheat cultivars. An increasing cell membrane permeability correlated with a decrease of RWC in ‘Banderola’ and ‘Komnata’. The content of proline under the increasing salinity correlated with changes of RWC in ‘Banderola’, ‘Komnata’ and line 121, which indicate protectoral role of proline against dehydration of tissue. Dry weight and RWC seem to be the parameters most useful in the salt-tolerance estimation of wheat plants. Taking into account the studied parameters ‘Banderola’ could be recognized as more salt tolerant, the degree of salinity tolerance of ‘Bogatka’ is the same as line 121, while ‘Komnata’ seems to be the most salt sensitive. The salt tolerance of T. aestivum and T. durum depends on the cultivar rather than the wheat species.     

Towards linkage analysis with markers in linkage disequilibrium by graphical modelling

We review recent developments of MCMC integration methods for computations on graphical models for two applications in statistical genetics: modelling allelic association and pedigree based linkage analysis. We discuss and illustrate estimation of graphical models from haploid and diploid genotypes, and the importance of MCMC updating schemes beyond what is strictly necessary for irreducibility. We then outline an approach combining these methods to compute linkage statistics when alleles at the marker loci are in linkage disequilibrium. Other extensions suitable for analysis of SNP genotype data in pedigrees are also discussed and programs that implement these methods, and which are available from the author's web site, are described. We conclude with a discussion of how this still experimental approach might be further developed.