Microsatellite mapping of the induced sphaerococcoid mutation genes in Triticum aestivum

The S1, S2 and S3 genes of the induced sphaerococcoid mutation in common wheat (Triticum aestivum) were mapped using three different F₂ populations consisting of 71–96 individual plants. Twenty-four microsatellite markers from homeologous group 3 of T. aestivum were used to map the S1, S2 and S3 genes on chromosomes 3D, 3B and 3A, respectively. The S1 locus was found to be closely linked to the centromeric marker Xgwm456 of the long arm (2.9 cM) and mapped not far (8.0 cM) from the Xgdm72 marker of the short arm of chromosome 3D. The S2 gene was tightly linked to 2 centromeric markers (Xgwm566, Xgwm845) of chromosome 3B. S3 was located between Xgwm2 (5.1 cM), the marker of the short arm, and Xgwm720 (6.6 cM), the marker of the long arm, both of chromosome 3A. Mapping the S1, S2 and S3 loci of the induced sphaerococcoid mutation near the centromeric regions supports the hypothesis that the sphaerococcum type may be due to gene duplication resulting from DNA recombination in the centromeric region. Received: 20 June 1999 / Accepted: 29 July 1999     

Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.)

The mature spike rachis of wild emmer [Triticum turgidum L. ssp. dicoccoides (Körn. ex Asch. and Graebner) Thell.] disarticulates spontaneously between each spikelet leading to the dispersion of wedge-type diaspores. By contrast, the spike rachis of domesticated emmer (Triticum turgidum L. ssp. turgidum) fails to disarticulate and remains intact until it is harvested. This major distinguishing feature between wild and domesticated emmer is controlled by two major genes, brittle rachis 2 (Br-A2) and brittle rachis 3 (Br-A3) on the short arms of chromosomes 3A and 3B, respectively. Because of their biological and agricultural importance, a map-based analysis of these genes was undertaken. Using two recombinant inbred chromosome line (RICL) populations, Br-A2, on chromosome 3A, was localized to a ~11-cM region between Xgwm2 and a cluster of linked loci (Xgwm666.1, Xbarc19, Xcfa2164, Xbarc356, and Xgwm674), whereas Br-A3, on chromosome 3B, was localized to a ~24-cM interval between Xbarc218 and Xwmc777. Comparative mapping analyses suggested that both Br-A2 and Br-A3 were present in homoeologous regions on chromosomes 3A and 3B, respectively. Furthermore, Br-A2 and Br-A3 from wheat and Btr1/Btr2 on chromosome 3H of barley (Hordeum vulgare L.) also were homoeologous suggesting that the location of major determinants of the brittle rachis trait in these species has been conserved. On the other hand, brittle rachis loci of wheat and barley, and a shattering locus on rice chromosome 1 did not appear to be orthologous. Linkage and deletion-based bin mapping comparisons suggested that Br-A2 and Br-A3 may reside in chromosomal areas where the estimated frequency of recombination was ~ 4.3 Mb/cM. These estimates indicated that the cloning of Br-A2 and Br-A3 using map-based methods would be extremely challenging.     

Microsatellite markers linked to 2 powdery mildew resistance genes introgressed from Triticum carthlicum accession PS5 into common wheat.

Two dominant powdery mildew resistance genes introduced from Triticum carthlicum accession PS5 to common wheat were identified and tagged using microsatellite markers. The gene designated PmPS5A was placed on wheat chromosome 2AL and linked to the microsatellite marker Xgwm356 at a genetic distance of 10.2 cM. Based on the information of its origin, chromosome location, and reactions to 5 powdery mildew isolates, this gene could be a member of the complex Pm4 locus. The 2nd gene designated PmPS5B was located on wheat chromosome 2BL with 3 microsatellite markers mapping proximally to the gene: Xwmc317 at 1.1 cM; Xgwm111 at 2.2 cM; and Xgwm382 at 4.0 cM; and 1 marker, Xgwm526, mapping distally to the gene at a distance of 18.1 cM. Since this gene showed no linkage to the other 2 known powdery mildew resistance genes on wheat chromosome 2B, Pm6 and Pm26, we believe it is a novel powdery mildew resistance gene and propose to designate this gene as Pm33.     

Genetic mapping of three alleles at the Pm3 locus conferring powdery mildew resistance in common wheat (Triticum aestivum L.).

A set of differential isolates of Blumeria graminis f.sp. tritici was used to identify 10 alleles at the Pm3 locus on the short arm of chromosome 1A. Three F3 populations were used to map Pm3h in Abessi, Pm3i in line N324, and Pm3j alleles in GUS 122 relative to microsatellite markers. In total, 13 marker loci were mapped on chromosome 1AS and 1 marker on 1AL. The order of marker loci in the 3 mapping populations is consistent with previously published maps. All 3 alleles were mapped in the distal region of chromosome 1AS. The present study indicated that microsatellite markers are an ideal marker system for comparative mapping of alleles at the same gene locus in different mapping populations. The linkage distances of the closest microsatellite marker, Xgwm905-1A, to Pm3h, Pm3i, and Pm3j were 3.7 cM, 7.2 cM, and 1.2 cM, respectively. The microsatellite marker Xgwm905-1A cannot be used to distinguish between Pm3 alleles. The development of specific markers for individual Pm3 alleles is discussed on the basis of the recently cloned Pm3b allele.     

Microsatellite mapping of the powdery mildew resistance gene <Emphasis Type="Italic">Pm5e</Emphasis> in common wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Powdery mildew, caused by Erysiphe graminis DM f. sp. tritici (Em. Marchal), is one of the most important diseases of common wheat world-wide. Chinese wheat variety 'Fuzhuang 30' carries the powdery mildew resistance gene Pm5e and has proven to be a valuable resistance source of powdery mildew for wheat breeding. Microsatellite markers were employed to identify the gene Pm5e in a F(2) progeny from the cross 'Nongda 15' (susceptible) x 'Fuzhuang 30' (resistant). The gene Pm5e was mapped in the distal region of chromosome 7BL. Seven microsatellite markers were found to be linked to the gene Pm5e, of which two codominant markers Xgwm783 and Xgwm1267 were relatively close to Pm5e with a linkage distance of 11.0 cM and 6.6 cM, respectively. It is possible to use the 136-bp allele of Xgwm1267 in 'Fuzhuang 30' for marker-assisted selection during the wheat resistance breeding process for facilitation of gene pyramiding. The mapping information in the present study provides a starting point for fine mapping of the Pm5 locus and map-based cloning to clarify the molecular structure and function of the different alleles at the Pm5 locus. A microsatellite linkage map of chromosome 7B was constructed with 20 microsatellite loci, nine on the short arm and 11 on the long arm. This information will be very useful for further mapping of agronomically important genes of interest on chromosome 7B.     

Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat

Two populations of single chromosome recombinant lines were used to map genes controlling flowering time on chromosome 5B of wheat, and one of the populations was also used to map a new frost resistance gene. Genetic maps were developed, mainly using microsatellite markers, and QTL analysis was applied to phenotypic data on the performance of each population collected from growth-room tests of flowering time and frost tolerance. Using a recombinant substitution-line mapping population derived from a cross between the substitution-line 'Chinese Spring' ('Cheyenne' 5B) and 'Chinese Spring' (CS), the gene Vrn-B1, affecting vernalization response, an earliness per se locus, Eps-5BL1, and a gene, Fr-B1, affecting frost resistance, were mapped. Using a 'Hobbit Sib' ('Chinese Spring' 5BL) x 'Hobbit Sib' recombinant substitution line mapping population, an earliness per se locus, Eps-5BL2 was mapped. The Vrn-B1 locus was mapped on the distal portion of the long arm of chromosome 5B, to a region syntenous with the segments of chromosomes 5A and 5D containing Vrn-A1 and Vrn-D1 loci, respectively. The two Eps-5BL loci were mapped close to the centromere with a 16-cM distance from each other, one in agreement with the position of a homoeologous locus previously mapped on chromosome 5H of barley, and suggested by the response of 'Chinese Spring' deletion lines. The Fr-B1 gene was mapped on the long arm of chromosome 5B, 40 cM from the centromeric marker. Previous comparative mapping data with rice chromosome 9 would suggest that this gene could be orthologous to the other Fr genes mapped previously by us on chromosomes 5A or 5D of wheat, although in a more proximal position. This study completes the mapping of these homoeoallelic series of vernalization requirement genes and frost resistance genes on the chromosomes of the homoeologous group 5 in wheat.     

Saturation and comparative mapping of a major Fusarium head blight resistance QTL in tetraploid wheat

Fusarium head blight (FHB) is a devastating disease of cultivated wheat worldwide. Partial resistance to FHB has been identified in common wheat (Triticum aestivum L.). However, sources of effective FHB resistance have not been found in durum wheat (T. turgidum L. var. durum). A major FHB resistance quantitative trait loci (QTL), Qfhs.ndsu-3AS, was identified on chromosome 3A of T. dicoccoides, a wild relative of durum wheat. Here, we saturated the genomic region containing the QTL using EST-derived target region amplified polymorphism (TRAP), sequence tagged site (STS), and simple sequence repeat (SSR) markers. A total of 45 new molecular marker loci were detected on chromosome 3A and the resulting linkage map consisted of 55 markers spanning a genetic distance of 277.2 cM. Qfhs.ndsu-3AS was positioned within a chromosomal interval of 11.5 cM and is flanked by the TRAP marker loci, Xfcp401 and Xfcp397.2. The average map distance between the marker loci within this QTL region was reduced from 4.9 cM in the previous study to 3.5 cM in the present study. Comparative mapping indicated that Qfhs.ndsu-3AS is not homoeologous to Qfhs.ndsu-3BS, a major FHB QTL derived from the common wheat cultivar Sumai 3. These results facilitate our efforts toward map-based cloning of Qfhs.ndsu-3AS and utilization of this QTL in durum wheat breeding via marker-assisted selection.     

High-density genetic and physical bin mapping of wheat chromosome 1D reveals that the powdery mildew resistance gene <Emphasis Type="Italic">Pm24</Emphasis> is located in a highly recombinogenic region

Genetic maps of wheat chromosome 1D consisting of 57 microsatellite marker loci were constructed using Chinese Spring (CS) × Chiyacao F₂ and the International Triticeae Mapping Initiative (ITMI) recombinant inbred lines (RILs) mapping populations. Marker order was consistent, but genetic distances of neighboring markers were different in two populations. Physical bin map of 57 microsatellite marker loci was generated by means of 10 CS 1D deletion lines. The physical bin mapping indicated that microsatellite marker loci were not randomly distributed on chromosome 1D. Nineteen of the 24 (79.2%) microsatellite markers were mapped in the distal 30% genomic region of 1DS, whereas 25 of the 33 (75.8%) markers were assigned to the distal 59% region of 1DL. The powdery mildew resistance gene Pm24, originating from the Chinese wheat landrace Chiyacao, was previously mapped in the vicinity of the centromere on the short arm of chromosome 1D. A high density genetic map of chromosome 1D was constructed, consisting of 36 markers and Pm24, with a total map length of 292.7 cM. Twelve marker loci were found to be closely linked to Pm24. Pm24 was flanked by Xgwm789 (Xgwm603) and Xbarc229 with genetic distances of 2.4 and 3.6 cM, respectively, whereas a microsatellite marker Xgwm1291 co-segregated with Pm24. The microsatellite marker Xgwm1291 was assigned to the bin 1DS5-0.70-1.00 of the chromosome arm 1DS. It could be concluded that Pm24 is located in the ‘1S0.8 gene-rich region’, a highly recombinogenic region of wheat. The results presented here would provide a start point for the map-based cloning of Pm24.     

Marker assisted genetic analysis of non-brittle rachis trait in barley

Brittle rachis is a head shattering mechanism of barley. Two tightly linked complementary genes, btr1 and btr2, were believed to control the non-brittle rachis trait. Position of non-brittle rachis loci btr1btr2 on the short arm of Chromosome 3 was investigated using RFLP markers. Two approaches were employed. First, a Hordeum vulgare subsp. spontaneum fragment that confers brittleness in a cv. Bowman near isogenic line was detected. This fragment is 18-33 cM in length and contains MWG798B, ABG057, MWG014, BCD706 and KFP216 markers of the short arm of Chromosome 3. In the second approach, position of btr1 locus in a H. vulgare subsp. spontaneum (Wadi Qilt 23-38)xH. vulgare subsp. vulgare (cv. Harrington) cross was detected using a selective genotyping approach in BC2F1 generation. F-tests and analysis of genotypic compositions of BC2F1 lines showed that btr1 locus, and supposedly the tightly linked btr2 locus, is in 4.3 cM KFP216-RisP114 interval of short arm of Chromosome 3. Results also yielded clues for the presence of at least two additional loci that affect the non-brittle rachis trait. Allelism tests using genotypes with known non-brittle rachis gene compositions provided additional evidence for presence of such loci.     

Identification of microsatellite markers linked to Russian wheat aphid resistance genes Dn4 and Dn6

The Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko), is a serious economic pest of wheat worldwide. Host plant resistance is the preferred method to control RWA infestations. The identification and mapping of RWA-resistant genes and the development of resistant wheat cultivars can be facilitated through the use of molecular markers. In the present study, microsatellite (SSR) markers linked to the RWA-resistant genes Dn4 and Dn6 were identified using several F(2) mapping populations derived from crosses of susceptible wheat cultivars and resistant sources. Two flanking microsatellite markers Xgwm106 and Xgwm337 are linked in coupling phase with Dn4 on the short arm of wheat chromosome 1D at 7.4 cM and 12.9 cM, respectively. Two other microsatellite markers Xgwm44 and Xgwm111 are linked to Dn6 in coupling phase near the centromere on the short arm of chromosome 7D at 14.6 cM and 3.0 cM, respectively. This is the first report on the chromosomal location of Dn6, which proved to be either allelic or tightly linked to Dn1, Dn2 and Dn5. This result of Dn6 location contradicts previous reports that Dn6 was independent of Dn1, Dn2 and Dn5. The linked markers can be conveniently used for marker-assisted selection in wheat breeding programs for the identification and/or pyramiding of Dn4 and Dn6 genes.     

Identification of microsatellite markers linked to leaf rust resistance gene <Emphasis Type="Italic">Lr25</Emphasis> in wheat

The leaf rust resistance gene Lr25, transferred from Secale cereale L. into wheat and located on chromosome 4B, imparts resistance to all pathotypes of leaf rust in South-East Asia. In an F₂-derived F₃ population, created by crossing TcLr25 that carries the gene Lr25 for leaf rust resistance with leaf rust-susceptible parent Agra Local, three microsatellite markers located on the long arm of chromosome 4B were found to be linked to the Lr25 locus. The donor parent TcLr25 is a near-isogenic line derived from the variety Thatcher. The most virulent pathotype of leaf rust in the South-East Asian region, designated 77–5 (121R63-1), was used for challenging the population under artificially controlled conditions. The marker Xgwm251 behaved as a co-dominant marker placed 3.8 cM away from the Lr25 locus on 4BL. Two null allele markers, Xgwm538 and Xgwm6, in the same linkage group were located at a distance of 3.8 cM and 16.2 cM from the Lr25 locus, respectively. The genetic sequence of Xgwm251, Lr25, Xgwm538, and Xgwm6 covered a total length of 20 cM on 4BL. The markers were validated for their specificity to Lr25 resistance in a set of 43 wheat genetic stocks representing 43 other Lr genes.     

Molecular marker assisted genetic analysis of head shattering in six-rowed barley

Head shattering in barley (Hordeum vulgare L.) has two forms; brittle rachis and weak rachis. Brittle rachis is not observed in cultivated barley since all cultivars carry non-brittle alleles at one of the two complementary brittle rachis loci (Btr1;Btr2). Weak rachis causes head shattering in barley cultivars and may be confused with brittle rachis. Brittle rachis has been mapped to the chromosome 3 (3H) short arm while map position(s) of the weak rachis is unknown. Two major and a putative minor QTL for head shattering were mapped using the Steptoe × Morex doubled haploid line population. The largest QTL, designated Hst-3, located on the chromosome 3 (3H) centromeric region, is associated with a major yield QTL. The Steptoe Hst-3 region, when transferred into Morex, resulted in a substantial decrease in head shattering. High-resolution mapping of Hst-3 was achieved using isogenic lines. Brittle rachis was mapped with molecular markers and shown to be located in a different position from that of Hst-3. The second major QTL, designated Hst-2 S, is located on chromosome 2 S. This locus is associated with an environmentally sensitive yield QTL.     

抗白粉病基因PmCH1302的遗传分析及染色体定位

CH1302是以来源于中间偃麦草的八倍体小偃麦TAI7047为桥梁亲本选育的高抗白粉病的小麦新品系,对白粉菌多个流行小种均表现出良好抗性。为了解其抗白粉病基因来源及其在染色体上的位置,对绵阳11×CH1302的F_1、F_2及F_(2∶3)家系进行了遗传分析,推断其抗白粉病基因可能来源于中间偃麦草,暂将其命名为PmCH1302。利用i Select 90K SNP芯片对抗、感病池进行扫描,发现位于2AL染色体上的多态性位点最多,为313个,占全部多态性位点的9.79%,且集中于2AL染色体100~105 c M和150~155 cM两个区域附近。在上述位点选取SSR标记,筛选出3对与Pm CH1302连锁的分子标记,Xwmc522、Xgwm356和Xgwm526,其中Xgwm356和Xgwm526位于Pm CH1302两侧,连锁距离分别为3.1 c M和7.8 cM。利用遗传图谱以及中国春缺体、双端体将PmCH1302定位于小麦2AL染色体上。进一步与位于2AL上的Pm4、Pm50比较发现,PmCH1302可能是位于2AL上的一个新基因或等位基因。     

Isolation of a chromosomally engineered durum wheat line carrying the Aegilops ventricosa pchl gene for resistance to eyespot.

The chromosome 7Dv of Aegilops ventricosa (syn. Triticum ventricosum, 2n = 4x = 28, genome DvDvMvMv) carries the gene Pch1 for resistance to eyespot. This gene has previously been transferred to chromosome 7D of bread wheat, T. aestivum (2n = 6x = 42, genome AABBDD). To (1) enhance the level of resistance of bread wheat by increasing the copy number of Pch1, and (2) create eyespot-resistant triticales, meiotically stable Pch1-carrying durum lines were selected from the backcross progenies of a cross between Ae. ventricosa and T. durum cv. Creso ph1c (2n = 4x = 28, genome AABB). The Pch1 transfer, likely resulting from homoeologous recombination, was located at the distal position on the long arm of chromosome 7A. The 7A microsatellite marker Xgwm 698 was found closely linked in repulsion to the introgression in the resistant recombination lines, and the endopeptidase allele located on chromosome 7A of cv. Creso ph1c was lost.     

普通小麦Qz180中一个抗条锈病基因的分子作图(英文)

普通小麦(Triticum aestivum L.)材料Qz180具有良好的抗条锈病特性,经基因推导发现其含有一个优良的抗条锈病的基因,暂定名为YrQz。用Qz180与感病材料铭贤169和WL1分别杂交构建了两个F_2群体,用条中30号条锈菌小种对这两个群体进行的抗性测验表明,YrQz为显性单基因遗传。通过SSR和AFLP结合BSA的方法对这个基因进行了分子作图,结果鉴定出与YrQz连锁的2个SSR标记和2个AFLP标记。根据SSR标记的染色体位置,该基因被定位在2B染色体的长臂上,位于两个SSR位点Xgwm388和Xgwm526之间;两个AFLP标记P35M48(452)和P36M61(163)分别位于该基因的两侧,遗传距离分别为3.4cM和4.1cM。     

Chromosome regions associated with the activity of lipoxygenase in the genome D of <Emphasis Type="Italic">Triticum aestivum</Emphasis> L. under water deficit

Quantitative trait loci (QTLs) associated with the phenotypic expression of the activity of different forms of lipoxygenase (LOX) under water deficit were detected in the chromosomes of the D-genome using intogression lines of common wheat Triticum aestivum L. Chinese Spring (Synthetic 6x). QTL associated with the activity of seed soluble LOX was identified on the short arm of chromosome 4D. The activity of membranebound form of enzyme in the seedlings was mapped to the short arm, while that of a soluble form was on the long arm of chromosome 5D. Two regions responsible for the activity of soluble LOX in the leaves were found on the short arm of chromosome 2D. Three QTLs associated with the activities of chloroplast LOXs were found on the same chromosome: the activity of the soluble form was linked to Xgwm261 and Xgwm539 markers, and the membrane form to Xgdm93 marker. QTLs for the activities of both soluble and membrane-bound LOX in the leaves were identified in the centromeric region of chromosome 7D. The activities of two membrane enzymes in the leaves were linked to Xgdm130 marker on the short arm of this chromosome. Loci associated with the activity of different LOX forms colocalized with QTLs for the shoot mass, gas exchange parameters, chlorophyll fluorescence, content of photosynthetic pigments, and grain productivity of wheat. A correlation between these parameters and the LOX activity was detected and it was shown that various forms of the enzyme were differentially involved in the adaptation of wheat plants to water deficit. The current paper discusses their presumed physiological role.     

普通小麦Qz180中一个抗条锈病基因的分子作图

普通小麦(Triticum aestivum L.)材料Qz180具有良好的抗条锈病特性,经基因推导发现其含有一个优良的抗条锈病的基因,暂定名为YrQz.用Qz180与感病材料铭贤169和WL1分别杂交构建了两个F2群体,用条中30号条锈菌小种对这两个群体进行的抗性测验表明,YrQz为显性单基因遗传.通过SSR和AFLP结合BSA的方法对这个基因进行了分子作图,结果鉴定出与YrQz连锁的2个SSR标记和2个AFLP标记.根据SSR标记的染色体位置,该基因被定位在2B染色体的长臂上,位于两个SSR位点Xgwm388和Xgwm526之间;两个AFLP标记P35M48(452)和P36M61(163)分别位于该基因的两侧,遗传距离分别为3.4 cM和4.1cM.     

易组"太谷核不育基因"(Ms2)基因定位的研究

将在远缘杂交中由普通小麦（AABBDD）4D染色体易组导入六倍体小黑麦（AABBRR）以及硬粒小麦（AABB）的太谷核不育基因Ms2（原位于普通小麦4D染色体短臂距着丝点31．2cM的显性雄性不育核基因）。重新异回普通小麦染色体组中,所获得携带易组Ms2基因的新型太谷核不育小麦其显性雄性不育特性表达正常,且雄性不育株的雌性可育机制正常,对不育株幼穗花粉母细胞减数分型期染色体构型的观察可见其为整倍体（2n=42),尚未发现回归普通小麦的易组太谷核不育与原位 的太谷核不育基因有不同的表型。采用系统的标志基因测交法对回归普通小麦的易组太谷不育基因进行测交定位,发现易组Ms2基因与普通小麦显性秆标志基因Rht3连锁,从而将其定位于普通小麦4B 色体虎Rht3基因9.7cM处,新位点被命名为Ms2（4BS）,对Ms2基因在六倍体小黑麦与原太谷核不育小麦远缘杂交中位时的走向,普通小麦4A与4B染色体的互换更名以及Ms2（4BS）新位点的开发利用进行了讨论,认为异源多倍体生物核基因的组间易位倾向于从供体染色体向进化亲缘关系较密切,且染色体序数与染色体臂相同的部分同源染色体易位;1988年第7届国际小麦遗传学会对普通小麦4A与4B染色体的互换更名是正确的;Ms2（4BS）作为一个新型的遗传标记,作为小麦族内所有携带B染色体组的物种的育种工具和在拓建各为小麦种质资源的基因库等方面均有广泛的用途。     

Genetic analysis of wheat domestication and evolution under domestication

Wheat is undoubtedly one of the world's major food sources since the dawn of Near Eastern agriculture and up to the present day. Morphological, physiological, and genetic modifications involved in domestication and subsequent evolution under domestication were investigated in a tetraploid recombinant inbred line population, derived from a cross between durum wheat and its immediate progenitor wild emmer wheat. Experimental data were used to test previous assumptions regarding a protracted domestication process. The brittle rachis (Br) spike, thought to be a primary characteristic of domestication, was mapped to chromosome 2A as a single gene, suggesting, in light of previously reported Br loci (homoeologous group 3), a complex genetic model involved in spike brittleness. Twenty-seven quantitative trait loci (QTLs) conferring threshability and yield components (kernel size and number of kernels per spike) were mapped. The large number of QTLs detected in this and other studies suggests that following domestication, wheat evolutionary processes involved many genomic changes. The Br gene did not show either genetic (co-localization with QTLs) or phenotypic association with threshability or yield components, suggesting independence of the respective loci. It is argued here that changes in spike threshability and agronomic traits (e.g. yield and its components) are the outcome of plant evolution under domestication, rather than the result of a protracted domestication process. Revealing the genomic basis of wheat domestication and evolution under domestication, and clarifying their inter-relationships, will improve our understanding of wheat biology and contribute to further crop improvement.     

Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat.

Bread wheat and durum wheat were examined for linkage disequilibrium (LD) using microsatellite markers distributed across the genome. The allele database consisted of 189 bread wheat accessions genotyped at 370 loci and 93 durum wheat accessions genotyped at 245 loci. A significance level of p < 0.001 was set for all comparisons. The bread and durum wheat collections showed that 47.9% and 14.0% of all locus pairs were in LD, respectively. LD was more prevalent between loci on the same chromosome compared with loci on independent chromosomes and was highest between adjacent loci. Only a small fraction (bread wheat, 0.9%; durum wheat, 3.2%) of the locus pairs in LD showed R2 values > 0.2. The LD between adjacent locus pairs extended (R2 > 0.2) approximately 2-3 cM, on average, but some regions of the bread and durum wheat genomes showed high levels of LD (R2 = 0.7 and 1.0, respectively) extending 41.2 and 25.5 cM, respectively. The wheat collections were clustered by similarity into subpopulations using unlinked microsatellite data and the software Structure. Analysis within subpopulations showed 14- to 16-fold fewer locus pairs in LD, higher R2 values for those pairs in LD, and LD extending further along the chromosome. The data suggest that LD mapping of wheat can be performed with simple sequence repeats to a resolution of <5 cM.