Genetic and physical mapping of photoperiod insensitive gene Ppd-B1 in common wheat

Photoperiod response is a major determinant of duration of growing stages in wheat. Conscious selection for these photoperiod response genes in plant breeding programs will yield genotypes with better adaptation to diverse environments. To provide a starting point for the development of molecular markers useful for the selection process, genetic maps around the photoperiod insensitive gene Ppd-B1 were built employing three segregating populations. Of 25 markers that were selected for the Ppd-B1 region, only two could be mapped across all three populations. In pairwise comparisons, the extent of transferable markers ranged from three to eight. Recombination frequencies of markers distal to Ppd-B1 were more homogeneous than those of proximal markers. This finding suggested a closer proximity of Ppd-B1 to the markers that were mapped distal to breakpoint 0.83 in the physical map of chromosome 2BS. This revised version was published online in August 2006 with corrections to the Cover Date.     

Association of RFLP markers with trait loci affecting clubroot resistance and morphological characters in Brassica oleracea L.

Summary Resistance to Plasmodiophora brassicae Wor. race 7, the causal agent of the disease clubroot, was examined in an F₂ population of a cross between a clubroot resistant broccoli (Brassica oleracea var. italica) and a susceptible cauliflower (B. oleracea var. botrytis). A genetic linkage map was constructed in the same population based on the segregation of 58 dispersed restriction fragment length polymorphism (RFLP) markers. Associations between the inheritance of RFLP marker genotypes and segregation for disease resistance, morphological and maturity characteristics were examined. For each triat examined, several chromosomal regions marked by RFLP probes appeared to contain trait loci, suggesting that each trait was under polygenic control. RFLP marker linkage to a major factor imparting dominance for clubroot resistance from the broccoli parent was observed in this population. Additionally, RFLP marker linkage to an independently segregating factor contributing clubroot resistance from the cauliflower parent was observed, indicating that it should be possible to use RFLP markers to facilitate selection of transgressive segregants having the combined resistance from both parental sources. In some instances, RFLP markers from the same or closely linked chromosomal regions were associated with both clubroot resistance and morphological traits. Analysis of RFLP marker genotypes at linked loci should facilitate the selection of desired disease resistant morphotypes.     

Molecular mapping of a new gene for resistance to rice blast (Pyricularia grisea Sacc.)

A single dominant blast resistance gene conferring resistance to a Korean rice blast isolate was identified in rice variety `Suweon 365'. We report the chromosomal localization and molecular mapping of this blast resistance gene designated as Pi-18, which confers resistance to Korean isolate `KI-313' of the blast pathogen. To know whether there is a relationship among genes conditioning resistance to location-specific isolates of the blast pathogen and thereby to identify linked markers to resistance gene for isolate KI-313 collected in Korea, RFLP markers previously reported to be linked to major blast resistance genes in different rice germplasm and other markers mapped to nearby regions were surveyed for polymorphism between a resistant (`Suweon 365') and a susceptible (`Chucheongbyeo') parent. Linkage associations of the RFLP markers with the resistance gene were verified using an F2 and F3 segregating population of known blast reaction. RFLP analysis showed that Pi-18 was located near the end of chromosome 11, linked to a single copy clone RZ536 at a distance of 5.4 centiMorgans (cM) and that this gene was different from Pi-1(t). An allelism test revealed that this gene was also different from Pi-k. Currently, a combination of RAPD and microsatellite primers is being employed to find additional markers in this region. Tightly linked DNA markers will facilitate selection for resistant genotypes in breeding programs and provide the basis for map based cloning of this new blast resistance gene. This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of root traits and phosphorus uptake in common bean (Phaseolus vulgaris L.) under limited soil phosphorus supply

Heterosis is an important way to improve yield and quality for many crops. Hybrid rice and hybrid maize contributed to enhanced productivity which is essential to supply enough food for the increasing world population. The success of hybrid rice in China has led to a continuous interest in hybrid wheat, even when most research on hybrid wheat has been discontinued in other countries for various reasons including low heterosis and high seed production costs. The Timopheevii cytoplasmic male sterile system is ideal for producing hybrid wheat seeds when fertility restoration lines with strong fertility restoration ability are available. To develop PCR-based molecular markers for use in marker-assisted selection of fertility restorer lines, two F₂ populations derived from crosses R18/ND36 and R9034/ND36 were used to map fertility restoration genes in the two elite fertility restorer lines (R-lines) R18 and R9034. Over 678 SSR markers were analyzed, and markers closely linked to fertility restoration genes were identified. Using SSR markers, a major fertility restoration gene, Rf3, was located on the 1B chromosome in both populations. This gene was partially dominant in conferring fertility restoration in the two restorer lines. SSR markers Xbarc207, Xgwm131, and Xbarc61 are close to this gene. These markers may be useful in marker-assisted selection of new restorer lines with T. timopheevii cytoplasm. Two minor QTL conferring fertility restoration were also identified on chromosomes 5A (in R18) and 7D (in R9034) in two R-lines.     

RFLP-based mapping of the Sec-2 and Sec-5 loci encoding 75K γ-secalins of rye

For mapping the Sec2 and Sec5 loci of rye which determine expression of 75K γ-secalins, a partial genetic map of chromosome 2R spanning 64 cM was constructed. The map was developed using an F₂ population of 103 plants from a cross between two inbred lines. Both loci were mapped distally on the short arm of chromosome 2R and clearly tagged in relation to 12 restriction fragment length polymorphism (RFLP) markers. The Sec2 locus was localized between the Xiag57 and Xpsr109a loci in an 11 cM interval. The Sec5 locus co-segregated to Xiag57 and was tightly linked to the Sec2 locus at a map distance of 0.5cM.     

Combining different linkage maps in sugar beet (Beta vulgaris L.) to make one map

Several genetic maps for sugar beet (Beta vulgaris L.), from different German research groups, have been published and it is now possible to consider combining them with the aid of the common markers. The computer program JOINMAP (versions 1.3 and 2.0) was used for pair-wise combination of three populations. Several problems arose: the genetic background of the populations, different population structures (F₂ versus F₁× F₁), different number of polymorphic loci for common probes in the populations to be combined, different estimates of the recombination rates between the same markers and differences between the Join Map versions. The maps from two F₂ populations could be integrated into a single map, but it was more appropriate to construct separate maps for the F₂ populations and the F₁× F₁ population using common markers as reference points only.     

A skeletal linkage map of Hordeum bulbosum L. and comparative mapping with barley (H. vulgare L.)

A restriction fragment length polymorphism (RFLP) based linkage map of a cross between two diploid Hordeum bulbosum (2n = 2x = 14) clones, PB1 and PB11, was constructed from 46 recombinant progeny clones. Since both parents are heterozygous, separate and combined parental maps were constructed. All of the RFLP markers screened had previously been mapped in barley (H. vulgare L.) so that comparative maps could be produced. The PB1 linkage map consists of 20 RFLP marker loci assigned to four linkage groups covering 94.3 cM. The PB11 linkage map consists of 27 RFLP marker loci assigned to six linkage groups covering 149.1 cM. Thirteen markers polymorphic in both parents were used as ‘anchors’ to create a combined linkage map consisting of 38 loci assigned to six linkage groups and covering a genetic distance of 198 cM. Marker order was highly conserved in a comparison with the linkage map of H. vulgare (Laurie etal., 1995). However, in contrast, the genetic distances for the same markers were very different being 649 cM and 198 cM respectively, a genetic distance ratio of 1: 3.3. Thus although the map was short, it can be presumed to cover half the genome of H. bulbosum. This study provides further confirmation of the close relationship between the two species and gives a basis for the development of marker mediated introgression through interspecific hybridisation between the two species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Construction of a linkage map for watermelon (Citrullus lanatus (Thunb.) Matsum & Nakai) using random amplified polymorphic DNA (RAPD)

Summary A linkage map for watermelon (Citrullus lanatus) was constructed on the basis of RADP, ribosomal DNA restriction fragment length polymorphism (RFLP), isozyme, and morphological markers using F₁BC1. A segregating population of 78 individuals was the result of a backcross of a cultivated inbred line (H-7; Citrullus lanatus; 2n=22) and a wild form (SA-1; C. lanatus; 2n=22), in which the latter was the recurrent (male) parent. A total of 69 RAPD, one RFLP, one isozyme, and three morphological markers was found to segregate in the BC1 population. Linkage analysis revealed that 62 loci could be mapped to 11 linkage groups that extended more than 524 centimorgans (cM), while 12 loci segregated independently of all other markers. The locus for exocarp color was linked to two RAPD markers within a region of 5 cM on linkage group 4. The locus for flesh color was linked to a RAPD marker within a region of 30 cM on linkage group 6. The isozyme marker GOT was located on the linkage group 1. Linkage group 2 contained a locus for ribosomal DNA within 5 cM of a RAPD marker. Half of the RAPD markers on the linkage group 7 displayed severely distorted segregation. The construction of linkage map using molecular markers is necessary for the breeding of watermelon to introduce useful gene of wild watermelon efficiently. However the linkage map that was constructed for the most part on the basis of RAPD markers could not cover significant parts of the genome, the linkage map provides breeders of watermelons the possibility of tagging useful agronomic traits, as well as the gene for exocarp color.Abbreviations RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism - GOT glutamate oxaloacetate transaminase - MDH malate dehydrogenase - ACP acid phosphatase - 6PGH 6-phosphogluconate dehydrogenase     

Localization of QTL for basal root thickness in <Emphasis Type="Italic">japonica</Emphasis> rice and effect of marker-assisted selection for a major QTL

Root traits are key components of plant adaptation to drought environment. By using a 120 recombined inbred lines (RILs) rice population derived from a cross between IRAT109, a japonica upland rice cultivar and Yuefu, a japonica lowland rice cultivar, a complete genetic linkage map with 201 molecular markers covering 1,833.8 cM was constructed and quantitative trait loci (QTLs) associated with basal root thickness (BRT) were identified. A major QTL, conferring thicker BRT, located on chromosome 4, designated brt4, explained phenotypic variance of 20.6%, was selected as target QTL to study the effects of marker-assisted selection (MAS) using two early segregating populations derived from crosses between IRAT109 and two lowland rice cultivars. The results showed that the flanking markers of brt4 were genetically stable in populations with different genetic backgrounds. In the two populations under upland conditions, the difference between the means of BRT of plants carrying positive and negative favorable alleles at brt4 flanking markers loci was significant. Phenotypic effects of BRT QTL brt4 were 5.05–8.16%. When selected plants for two generations were planted at Beijing and Hainan locations under upland conditions, MAS effects for BRT QTL brt4 were 4.56–18.56% and 15.46–26.52% respectively. The means of BRT for the homozygous plants were greater than that of heterozygous plants. This major QTL might be useful for rice drought tolerance breeding. L. Liu and P. Mu are contributed equally to this work.     

RFLP/AFLP mapping of a brown planthopper (Nilaparvata lugens Stål) resistance gene Bph1 in rice

We have constructed a linkage map of the rice brown planthopper (BPH)resistance gene, Bph1. RFLP and AFLP markers were selected by thebulked segregant analysis and used in the mapping study of 262 F₂sthat were derived from a cross of `Tsukushibare', a susceptible japonica cultivar, and `Norin-PL3', an authentic japonicaBph1-introgression line. Twenty markers were mapped within a 28.9-cMregion containing the Bph1 locus on the long arm of rice chromosome12. Combining the result of segregation analysis of BPH resistance by themass seedling test and that of the markers, the Bph1 locus wasmapped within a 5.8-cM region between two flanking markers. The closestAFLP markers, em5814N and em2802N, was at 2.7 cM proximal to theBph1 locus. Together with the previously constructed high-resolutionmap of bph2 locating the locus at ca. 10 cM proximal to the Bph1 locus, this improved version of the linkage map would facilitatepyramiding these two important BPH resistance genes.     

Comparisons of RFLP and PCR-based markers to detect polymorphism between wheat cultivars

Previously chromosome 3A of wheat (Triticum aestivum L.) was reported to carry genes influencing yield, yield components, plant height, and anthesis date. The objective of current study was to survey various molecular marker systems for their ability to detect polymorphism between wheat cultivars Cheyenne(CNN) and Wichita (WI), particularly for chromosome3A. Seventy-seven `sequence tagged site' (STS), 10simple sequence repeat (SSR), 40 randomly amplified polymorphic DNA (RAPD) markers, and 52 restriction fragment length polymorphism (RFLP) probes for wheat homoeologous group 3 chromosomes, were investigated. Three (3.9%) STS-PCR primer sets amplified polymorphic fragments for the two cultivars, of which one was polymorphic for chromosome 3A. Sixty percent of SSR markers detected polymorphism between CNN and WI of which 50% were polymorphic for chromosome 3A. Twenty percent of RAPD markers detected polymorphism between CNN and WI in general, but none of these detected polymorphism for chromosome 3A. Of the fifty-two RFLP probes, 78.8% detected polymorphism between CNN and WI for group 3 chromosomes with one or more of seven restriction enzymes and 42% of the polymorphic fragements were for chromosome 3A. These high levels of RFLP and SSR polymorphisms between two related wheat cultivars could be used to map and tag genes influencing important agronomic traits. It may also be important to reconsider RFLP as the most suitable marker system at least for anchor maps of closely related wheat cultivars. This revised version was published online in July 2006 with corrections to the Cover Date.     

利用3个F_2群体整合高密度栽培种花生遗传连锁图

遗传图谱的构建及整合是开展花生分子育种研究的基础,利用多个作图群体整合遗传图谱是解决图谱标记密度低的有效途径。本研究采用基于锚定SSR标记的作图策略,构建3个F_2群体3张遗传连锁图,利用Join Map 3.0软件整合图谱,获得一张包含20个连锁群、792个位点、总遗传距离为2079.50 c M,标记间平均距离为2.63 c M的整合图谱,各连锁群标记数在20~66个之间,遗传距离在59.10~175.80 c M之间。将3个分离群体中检测到的与荚果及种子大小相关的QTL区段与整合连锁图的标记比较发现,各群体中检测到的位于各染色体上的QTL在整合图谱中都能出现,有些QTL标记区间在整合图谱中存在更多的标记,为今后利用这些标记进行精细定位奠定了基础。     

水稻RFLP连锁图谱的构建及控制小穗不育和花粉不育的QTL分析

用台中65(粳稻)/ARC10313(籼稻)的重组近交系(F10)构建了RFLP连锁图谱, 含113个分布均匀的标记. 作成的图谱覆盖全基因组, 全图总长1462.4 cM, 图中标记位置与所使用的参照图谱基本符合. 利用该重组自交家系材料与亲本台中65回交得到BF1家系, 用于对小穗不育和花粉不育的QTL分析, 检测出3个小穗不育和1个花粉不育QTL, 且有一     

Genetic and molecular organization of the short arm and pericentromeric region of tomato chromsome 6

We have previously presented an integrated linkage map of tomato chromosome 6, that showed the position of restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) markers relative to a variety of classical markers. As for the short arm, map resolution has now been improved by crossing the chromosome 6 substitution line WSL6 to additional tester lines, carrying markers on the short arm. Molecular linkage analysis of the F₂ populations enabled us to produce an integrated linkage map showing the position of molecular markers relative to the classical markers Aps-1, yv, Mi, Cf-2/Cf-5, tl and pds. In order to incorporate the centromere into the integrated map, a radiation-induced deletion mapping strategy was applied, using irradiated pollen from L. pennellii LA716 in crosses to a L. esculentum line recessive for the markers yv and tl, that flank the centromere. Molecular analysis of the hemizygous yv-deletion and tl-deletion plants identified among the F₁ progeny, provided an estimate of the size of the respective deletions and, thus, of the position of the centromere relative to the molecular markers linked to yv and tl. This radiation mapping approach also provided evidence showing that, unlike published data, the root knot nematode resistance gene Mi as well as the Cladosporium fulvum resistance genes Cf-2/Cf-5 are located on the short arm.     

Intrachromosomal mapping of genes for dwarfing (Rht12) and vernalization response (Vrn1) in wheat by using RFLP and microsatellite markers

For intrachromosomal mapping of the dominant GA-sensitive dwarfing gene Rht12 and the vernalization response gene Vrn1 on chromosome 5 A, an F₂ population was established using a wide (synthetic) wheat cross. In addition to restriction fragment length polymorphism (RFLP) probes four microsatellite markers were incorporated. Rht12 was mapped distally to four RFLP loci (Xmwg616, Xpsr164, Xwg114, Xpsr1201) and three microsatellite markers (Xgwm179, Xgwm410, Xgwm291), known to be located on the segment of chromosome SAL which was ancestrally translocated and is homoeologous to Triticeae 4 L. The map position of Rht12 suggests that it is homoeologous to the dominant GA-sensitive dwarfing gene Ddw1, present on chromosome 5RL. The vernalization response gene Vrn1 showed linkage to Xwg644, as might be expected from comparative maps.     

Molecular mapping of S-c, an F1 pollen sterility gene in cultivated rice

Hybrids between indica and japonica rice varieties usually show partial sterility, and are a major limiting factor in the utilization of heterosis at subspecific level. When studying male-gamete (pollen) abortion, a possibly important cause for sterility, six loci (S-a, S-b, S-c, S-d, S-e and S-f) for F₁ pollen sterility were identified. Here we report genetic and linkage analysis of S-c locus using molecular markers in a cross between Taichung 65, a japonica variety carrying allele S-c ^j, and its isogenic line TISL5, carrying alleleS-c ^j. Our results show that pollen sterility occurring in the hybrids is controlled by one locus. We used 208 RFLP markers, as well as 500 RAPD primers, to survey the polymorphism between Taichung 65 and TISL5. Six RFLP markers located on a small region of chromosome 3, detected different RFLP patterns. Co-segregation analysis of fertility and RFLP patterns with 123 F₂ plants confirmed that the markers RG227, RG391, R1420 were completely linked with the S-c locus. The genetic distances between the markers C730, RG166 and RG369 and the S-c locus were 0.5 cM, 3.4 cM, and 3.4 cM respectively. Distorted F₂ ratios were also observed for these 4 RFLP markers in the cross. This result suggests that the `one locus sporo-gametophytic' model could explain F₁ hybrid pollen sterility in cultivated rice. RG227, the completely linked marker, has been converted to STS marker for marker-assisted selection. This revised version was published online in August 2006 with corrections to the Cover Date.     

QTLs identification of crude fat content in brown rice and its genetic basis analysis using DH and two backcross populations

Fat content is a concern for the enhancement of rice for eating, cooking, and storage qualities. To clarify its genetic mechanism, a double haploid (DH) population derived from anther hybrid F₁ of Zhenshan 97B (indica) and Wuyujing 2 (japonica) and two backcross F₁ (BCF₁) populations, which came from the DH lines backcrossing to two parents, were used to scan quantitative trait loci (QTLs) and dissect gene effects for the crude fat content (CFC) in brown rice. Fourteen QTLs were resolved, distributing on chromosomes 1, 3, and 5–9. Three loci were detected repeatedly in two populations, DH or BCF₁. Among these loci, a major QTL, qCFC5, flanking markers RM87 and RM334, was located on chromosome 5, which was detected simultaneously among three populations. The main QTLs had a major role in controlling CFC in brown rice and were modified by several mini-effect QTLs and epistatic affection. Wenjun Liu and Jing Zeng are contributed equally to this paper.     

Molecular marker analysis of genetic variation characterizing a grasspea (Lathyrus sativus) collection from central Italy

Levels of genetic similarity characterizing 20 grasspea (Lathyrus sativus L.) populations collected in central Italy (17 populations in the Marche region and three populations in the Abruzzo region) were analysed with amplified fragment length polymorphism (AFLP) molecular markers. Two main clusters were found: one included large‐seeded populations from farms that were not market‐oriented (named Household populations) and the second, small‐seeded populations, cultivated in market‐oriented farms (named Commercial populations). Relationships among populations collected in different regions were found, although one population of the Abruzzo region was placed between the two main clusters, suggesting a possible further genetic differentiation within this grasspea germplasm collection. Principal component analysis based on AFLP marker frequency was effective in identifying polymorphic markers showing high discriminating ability between clusters H and C. In particular, seven markers showing high positive and three markers with low negative PC1 scores showed an almost cluster‐specific distribution. These results will be useful for enhancing Italian grasspea germplasm use in plant‐breeding programmes and for extending grasspea cultivation within the sustainable agricultural systems of central Italy.     

QTL for rice grain quality based on a DH population derived from parents with similar apparent amylose content

A doubled haploid (DH)population consisting of 135 lines, derived from an indica (IR64) and a japonica (Azucena) rice with a similar apparent amylose content (AAC), was used to investigate the genetic factors affecting cooking and eating quality of rice. AAC,gelatinization temperature (GT), gel consistency (GC) and six starch pasting viscosity parameters were measured for quantitative trait loci (QTL) analysis using 193 molecular markers mapped on the DH population. A total of 17 QTLs were detected for the 9 traits, with at least one QTL and as many as 3 QTLs for each individual trait. No QTL for the measured parameters was found at the wx locus,possibly because of the similar AAC between the parents. Several QTLs with important effects on the variations in the measured parameters were detected in the present study which have not been found in earlier reports based on populations derived from parents with different AAC and wxgene alleles. Two interesting loci could be deduced from the present study according to the marker order compared with other genetic linkage maps. A QTL flanked by Amy2A and RG433 on the end of the long arm of chromosome 6, identified for GT, set back and consistency viscosity, might cover the gene encoding starch branching enzyme I. Similarly, a QTL flanked by RG139 and RZ58on chromosome 2, detected for hot paste viscosity and breakdown viscosity, might cover the gene encoding starch branching enzyme III. Generally, traits significantly correlated with each other shared identical QTL, but it was not true in some cases. The fine molecular mechanisms underlying these traits await further elucidation for the improvement of eating and cooking quality of rice. This revised version was published online in August 2006 with corrections to the Cover Date.     

Tagging of four fertility restorer loci for wild abortive—cytoplasmic male sterility system in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) using microsatellite markers

Tagging of restorer genes for wild abortive (WA) CMS source by studying a 222 individual plants from a F₂ population of a cross between IR58025A × IR42686R. The restorer line IR42686R that was used in this study had been previously derived through random mating composite population (RMCP) involving 12 parents facilitated by IR36 genetic male sterility. Four Rf genes were tagged to simple sequence repeats (SSR) markers on chromosomes 1, 7, 10, 12 by recessive class analysis. The recombination frequency between a positive marker and Rf locus was calculated using maximum likelihood estimator assuming that all the 46 extremely sterile individual plants were homozygous at the targeted Rf locus. The recombination frequency between the marker and the restorer trait were converted to genetic distances using Kosambi function. A new Rf locus designated as Rf7 on chromosome 12 was found to be linked to RM7003 at a genetic distance of 13.3 cM (LOD 6.12). We report here first, a new molecular marker (RM 6344) linked to Rf4 locus on chromosome 7 that was previously mapped by trisomic analysis. RM443 and RM315 were flanking the Rf3 gene at a genetic distance of 4.4 (LOD 10.29) and 20.7 cM (LOD 3.98) on chromosome 1, respectively. The Rf6 was flanked on both side with SSR markers RM258 and RM591 at a genetic distance of 4.4 (LOD 10.29) and 23.3 cM (LOD 3.39) located on chromosome 10. The random mating composite population is an excellent breeding approach to develop superior restorer lines and for pyramiding different Rf genes of different CMS systems. Rf genes tagged with closely linked SSR markers would be facilitating marker assisted selection (MAS) in hybrid rice breeding program by reducing time and workload for identifying potential restorers. L. Bazrkar and A. J. Ali equally contributed to this work.