Detection of quantitative trait locus for leaffolder (Cnaphalocrocis medinalis (Guenée)) resistance in rice on linkage group 1 based on damage score and flag leaf width

Rice leaffolder (RLF) (Cnaphalocrocis medinalis (Guenée) is a destructive and widespread insect pest throughout the rice growing regions in Asia. The genetics of resistance to RLF in rice is very complex and not thoroughly explored. The present study was conducted to detect the quantitative trait loci (QTL) associated with RLF resistance involving 176 recombinant inbred lines (RILs) of F₈ generation derived from a cross between IR36, a leaffolder susceptible variety and TNAULFR831311, a moderately resistant indica rice culture. Simple sequence repeat (SSR) markers were used to construct specific linkage groups of rice. All the RILs were screened to assess their level of resistance to RLF by measuring the leaf area damaged. Besides this, the length and width of the flag leaf of each RIL were measured since these two parameters were considered as correlated traits to the RLF resistance in rice. All the above parameters observed across the RILs showed quantitative variation. Correlation analysis revealed that damage score based on greenhouse screening was positively correlated with length and width of the flag leaf. Out of 364 SSR markers analysed, 90 were polymorphic between the parents. Multi-point analysis carried out on segregating 69 SSR marker loci linkage group wise resulted in construction of linkage map with eleven groups of 42 SSR markers. Through single marker analysis, 19 SSR markers were found to have putative association with the three phenotypic traits studied. Of these markers, RM472 was identified as a locus having major effect on RLF resistance trait based on length of the flag leaf. Interval mapping detected two QTLs on linkage group 1. Among these QTLs, the QTL flanked by RM576–RM3412 were found to be associated with width of the flag leaf and RLF resistance. The putative SSR markers associated with leaffolder resistance identified in the present study may be one of the loci contributing resistance to RLF in rice.     

DNA typing of hops (Humulus lupulus) through application of RAPD and microsatellite marker sequences converted to sequence tagged sites (STS)

Summary Both random amplified polymorphic DNA and microsatellite repeat sequences were investigated as DNA markers for distinguishing hop cultivars. Microsatellite sequences converted to STS markers proved to be most successful. The relative abundance of microsatellite repeat sequences in the hop genome varied depending on the sequence class. Of the repeat types investigated the dinucleotide repeats (GA)_n and (GT)_n are the most highly represented in the hop genome. Microsatellite repeat sequences in hops have been shown to be highly polymorphic and are very informatives as STS molecular markers. A DNA typing system using sequence-tagged microsatellite site markers has been developed which will not only be useful for hop cultivar identification but also marker assisted breeding and quality control purposes.     

Development of pepper SSR markers from sequence databases

Simple sequence repeat (SSR) markers are potentiallyvaluable tools for plant breeding. The objectives ofthe work reported here were to search the EMBL andGenbank databases for the presence of SSR-containingsequences from the genus Capsicum, to assess thefrequency of different motifs, and to examine thepolymorphism of selected markers in a panel ofgenotypes, including 10 Capsicum spp. and 1tomato and 1 potato genotype. Fifty-eightmicrosatellites with different motifs were found inCapsicum sequences. A subset of twelve of thesewere selected for the polymorphism survey using PCRprimers flanking the SSR. Polymorphisms between Capsicum lines can be detected with 5 of these primerpairs. PCR products of the predicted size were alsoamplified with three primer pairs in potato and oneprimer pair in tomato. The study also showed thatshorter microsatellites could be valuable markers inCapsicum.     

Development and validation of microsatellite markers linked to the rice blast resistance gene <Emphasis Type="Italic">Pi-z</Emphasis> of Fukunishiki and Zenith

Rice blast resistance gene ‘Pi-z’ present in rice genotypes, Zenith and Fukunishiki, represents a potential source of blast resistance for the north-western Himalayan region of India. We tested the reliability of microsatellite markers linked to Pi-z for assessing blast resistance phenotype in crosses of commercial importance. A new set of microsatellite markers linked to Pi-z was also developed by exploiting the publicly available marker and genomic resources of rice. Of the three previously reported markers for Pi-z, only MRG5836 was suitable for the marker assisted selection of Pi-z. Among the 17 microsatellites selected from the putative region of Pi-z locus, two, RM8225 and RM8226 cosegregated with MRG5836 and were located at distance of 1.2–4.5 cM from the gene. A new microsatellite marker ‘SSR236’ was developed from the (CT)₁₆ repeat of PAC clone P0502B12, which exhibited closer linkage (0.6–1.2 cM) to Pi-z. Survey of the allelic diversity at the loci of the Pi-z linked microsatellite markers revealed that the Fukunishiki and Zenith type alleles were not present in majority of the local indica rice genotypes. As these markers are polymorphic between the Pi-z donors and a great majority of local indica rices tested, they can be used as a selection tool in rice breeding programs aimed at improving the blast resistance of local rices.     

Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP,ISSR and SSR markers

Molecular markers provide novel tools to differentiate between the various grades of Basmati rice, maintain fair-trade practices and to determine its relationship with other rice groups in Oryza sativa. We have evaluated the genetic diversity and patterns of relationships among the 18 rice genotypes representative of the traditional Basmati, cross-bred Basmati and non-Basmati (indica and japonica) rice varieties using AFLP, ISSR and SSR markers. All the three marker systems generated higher levels of polymorphism and could distinguish between all the 18 rice cultivars. The minimum number of assay-units per system needed to distinguish between all the cultivars was one for AFLP, two for ISSR and five for SSR. A total of 171 (110 polymorphic), 240 (188 polymorphic) and 160 (159 polymorphic) bands were detected using five primer combinations of AFLP, 25 UBC ISSR primers and 30 well distributed, mapped SSR markers, respectively. The salient features of AFLP, ISSR and SSR marker data analyzed using clustering algorithms, principal component analysis, Mantel test and AMOVA analysis are as given below: (i) the two traditional Basmati rice varieties were genetically distinct from indica and japonica rice varieties and invariably formed a separate cluster, (ii) the six Basmati varieties developed from various indica × Basmati rice crosses and backcrosses were grouped variably depending upon the marker system employed; CSR30 and Super being more closer to traditional Basmati followed by HKR228, Kasturi, Pusa Basmati 1 and Sabarmati, (iii) AFLP, ISSR and SSR marker data-sets showed moderate levels of positive correlation (Mantel test, r = 0.42–0.50), and (iv) the partitioning of the variance among and within rice groups (traditional Basmati, cross-bred Basmati, indica and japonica) using AMOVA showed greater variation among than within groups using SSR data-set, while reverse was true for both ISSR and AFLP data-sets. The study emphasizes the need for using a combination of different marker systems for a comprehensive genetic analysis of Basmati rice germplasm. The high-level polymorphism generated by SSR, ISSR and AFLP assays described in this study shall provide novel markers to differentiate between traditional Basmati rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.The first two authors have equal contribution     

Isolation of 1,796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum)

Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. To establish a genetic basis for molecular breeding of bunching onion, we isolated 1,796 simple sequence repeat (SSR) clones by large-scale sequencing of SSR-enriched genomic DNA libraries. Of these, 1,331 (74.1%) contained (GT) _n repeats (n > 5), while 314 (17.5%) were (GA) _n -containing clones. The average number of SSR repeats was 10.5 and 10.4 in the (GT) _n - and (GA) _n -containing clones, respectively. In a sample of five bunching onion inbred lines, an average of 3.2 alleles were detected in the 100 SSR loci investigated, with the polymorphic information content averaging 0.55. These results indicate that bunching onion SSRs are very rich sources of highly informative genetic markers.     

Mapping of the leaf rust resistance gene <Emphasis Type="Italic">Lr38</Emphasis> on wheat chromosome arm 6DL using SSR markers

Leaf rust caused by the fungus Puccinia triticina is one of the most important diseases of wheat (Triticum aestivum) worldwide. The use of resistant wheat cultivars is considered the most economical and environment-friendly approach in controlling the disease. The Lr38 gene, introgressed from Agropyron intermedium, confers a stable seedling and adult plant resistance against multiple isolates tested in Europe. In the present study, 94 F₂ plants resulting from a cross made between the resistant Thatcher-derived near-isogenic line (NIL) RL6097, and the susceptible Ethiopian wheat cultivar Kubsa were used to map the Thatcher Lr38 locus in wheat using simple sequence repeat (SSR) markers. Out of 54 markers tested, 15 SSRs were polymorphic between the two parents and subsequently genotyped in the population. The P. triticina isolate DZ7-24 (race FGJTJ), discriminating Lr38 resistant and susceptible plants, was used to inoculate seedlings of the two parents and the segregating population. The SSR markers Xwmc773 and Xbarc273 flanked the Lr38 locus at a distance of 6.1 and 7.9 cM, respectively, to the proximal end of wheat chromosome arm 6DL. The SSR markers Xcfd5 and Xcfd60 both flanked the locus at a distance of 22.1 cM to the distal end of 6DL. In future, these SSR markers can be used by wheat breeders and pathologists for marker assisted selection (MAS) of Lr38-mediated leaf rust resistance in wheat.     

A quantitative trait locus influencing tolerance to Phytophthora root rot in the soybean cultivar ‘Conrad’

‘Conrad’, a soybean cultivar tolerant to Phytophthora root rot (PRR), and ‘OX760-6-1’, a breeding line with low tolerance to PRR, were crossed. F₂ derived recombinant inbred lines were advanced to F₆ to generate a population through single-seed descent. This population was used to identify quantitative trait loci (QTLs) influencing PRR tolerance in ‘Conrad’. A total of 99 simple sequence repeat (SSR), or microsatellite, markers that were polymorphic and clearly segregated in the F₆ mapping population were used for QTL detection. Based on the data of PRR in the field at two planting locations, Woodslee and Weaver, for the years 2000 and 2001, one putative QTL, designated as Qsatt414-596, was detected using MapMaker/QTL. Qsatt414-596 was flanked by two SSR markers from the linkage group MLG J, Satt414 and Satt596. Satt414 and Satt596 were also detected to be significantly (P < 0.005) associated with PRR using the SAS GLM procedure and were estimated to explain 13.7% and 21.5% of the total phenotypic variance, respectively.     

Genetic analysis of partial resistance to coffee leaf rust ( Hemileia vastatrix Berk & Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species

The objective of this study was to identify polymorphic molecular markers associated with partial resistance to coffee leaf rust, Hemileia vastarix. A segregating F ₂ population derived from a cross between the susceptible Coffea arabica cv. Caturra and a C. canephora-introgressed Arabica line exhibiting high partial resistance was analyzed. Rust resistance measured as rust incidence (RI) and defoliation (DEF) was evaluated in field conditions in three consecutive years (2003–2005). During the 2003 season, which was characterized by favorable conditions for a rust epidemic, the F ₂ plants exhibited different levels of resistance ranging from very susceptible (50.1% for DEF and 49.5% for RI) to highly partial resistance (9.1% for DEF and 3.7% for RI). Molecular analysis enabled identification of seven polymorphic markers (5 AFLP and 2 SSR) exhibiting significant association with partial resistance. Coexistence of resistance homozygous alleles (RR) at codominant SSR loci was correlated with high resistance. This study is the first attempt to develop PCR-based sequence specific markers linked to partial rust resistance in coffee.     

SSR analysis of chromosome 8 regions associated with aroma and cooked kernel elongation in Basmati rice

Aroma and cooked kernel elongation (CKE) are the two most important quality traits, which differentiate the highly valued Basmati rice from other rice types. Previous studies on genetic analysis have shown that genes/QTLs for these two traits are linked and present on chromosome number 8. We have evaluated the genetic diversity in 33 rice genotypes representative of the traditional Basmati (TB), cross-bred Basmati derived from indica × Basmati rice crosses and non-Basmati (indica and japonica) rice varieties for chromosome number 8 using 26 SSR markers including a specific marker (SCU-SSR1) for RG28 locus; the results have been compared with whole genome based SSR allelic data. The 26 SSR markers (24 polymorphic and 2 monomorphic) amplified a total of 106 alleles; 21 of these alleles were detected to be unique, present in only one genotype. The number and size of the alleles, and polymorphism information content (PIC) values ranged between 1–8, 87–312 and 0–0.736 bp, respectively. SCU-SSR1 marker amplified a total of three alleles (128, 129 and 130 bp). All the TB varieties except Basmati 217 (129 bp) and 7/13 cross-bred Basmati varieties had the 130 bp allele. Alleles of 129 and 128 bp were present in majority of the indica and japonica varieties, respectively. The average pair-wise Jaccard similarity coefficients for TB, indica and japonica varieties were 0.512, 0.483 and 0.251, respectively. Average similarity coefficient between TB and japonica was higher (0.236) compared to that between TB and indicas (0.150). Genetic relationships as determined by Principal Component Analysis (PCA, NTSYS-pc), PowerMarker tree, and Structure analyses, clearly showed high-level differentiation between TB and indica rice varieties, which formed two distinct clusters. The cross-bred Basmati and japonica rice genotypes were placed between these two clusters. Basmati 217 and Ranbir Basmati were quite divergent from rest of the TB varieties. Some of cross-bred Basmati varieties including Super, CSR30 and kernel were closer to TB. Indica rice varieties, CSR10 (salt tolerant variety) and Pokkali (salt tolerant landrace) formed a separate distinct cluster. The Pritchard structure analysis divided the rice genotypes in four major sub-populations of TB, cross-bred Basmati, indica and japonica (including Ranbir Basmati and Basmati 217) rice varieties. Chromosome 8 data-set showed a positive correlation (Mantel test, r = 0.739) with the allelic data-set for 30 SSR markers well-distributed on 12 rice chromosomes indicating a higher level of similarity between the two. The study demonstrates the distinctness of TB from other rice types (indica and japonica) and also provides several novel markers for differentiation between TB rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.     

Development of high yielding IR64 × <Emphasis Type="Italic">Oryza rufipogon</Emphasis> (Griff.) introgression lines and identification of introgressed alien chromosome segments using SSR markers

Modern rice varieties that ushered in the green revolution brought about dramatic increase in rice production worldwide but at the cost of genetic diversity at the farmers’ fields. The wild species germplasm can be used for broadening the genetic base and improving productivity. Mining of alleles at productivity QTL from related wild species under simultaneous backcrossing and evaluation, accompanied by molecular marker analysis has emerged as an effective plant breeding strategy for utilization of wild species germplasm. In the present study, a limited backcross strategy was used to introgress QTL associated with yield and yield components from Oryza rufipogon (acc. IRGC 105491) to cultivated rice, O. sativa cv IR64. A set of 12 BC₂F₆ progenies, selected from among more than 100 BC₂F₅ progenies were evaluated for yield and yield components. For plant height, days to 50% flowering and tillers/plant, the introgression lines did not show any significant change compared to the recurrent parent IR64. For yield, 9 of the 12 introgression lines showed significantly higher yield (19–38%) than the recurrent parent IR64. Four of these lines originating from a common lineage showed higher yield due to increase in grain weight and another three also from a common lineage showed yield increase due to increase in grain number per panicle. For analyzing the introgression at molecular level all the 12 lines were analyzed for 259 polymorphic SSR markers. Of the total 259 SSR markers analyzed, only 18 (7.0%) showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6 and 11. Graphical genotypes have been prepared for each line and association between the introgression regions and the traits that increased yield is reported. Based on marker trait association it appears that some of the QTL are stable across the environments and genetic backgrounds and can be exploited universally.     

Development and utilization of novel SSRs in foxtail millet [Setaria italica (L.) P. Beauv.]

Although the foxtail millet [Setaria italica (L.) P. Beauv.] is recently regarded as a model crop for studying functional genomics of biofuel grasses, its genetic improvement to some extent was limited due to the non‐availability of molecular markers, particularly the microsatellite markers and the saturated genetic linkage map. Considering this, we attempted to generate a significant number of microsatellite markers in cultivar ‘Prasad’. Two hundred and fifty‐six clones were sequenced to generate 41.82‐kb high‐quality sequences retrieved from genomic library enriched with dinucleotide repeat motifs. Microsatellites were identified in 194 (76%) of the 256 positive clones, and 64 primer pairs (pp) were successfully designed from 95 (49%) unique SSR‐containing clones. The 67.4% primer designing ability, 100% PCR amplification efficiency and 45.3% polymorphic potential in the parents of F₂ mapping population established the efficacy of genomic microsatellites. All the 64 microsatellite markers displayed high level of cross‐species amplification (~67%) in 10 millets and non‐millets species. These experimental findings suggest the utility and efficacy of SSRs in diverse genotyping applications, resolving QTLs, phylogenetic relationships and transferability in several important grass species.     

Genetic mapping of AFLP markers in Japanese bunching onion (<Emphasis Type="Italic">Allium fistulosum</Emphasis>)

Summary The first genetic linkage map of Japanese bunching onion (Allium fistulosum) based primarily on AFLP markers was constructed using reciprocally backcrossed progenies. They were 120 plants each of (P₁)BC₁ and (P₂)BC₁ populations derived from a cross between single plants of two inbred lines: D1s-15s-22 (P₁) and J1s-14s-20 (P₂). Based on the (P₂)BC₁ population, a linkage map of P₁ was constructed. It comprises 164 markers – 149 amplified fragment length polymorphisms (AFLPs), 2 cleaved amplified polymorphic sequences (CAPSs), and 12 simple sequence repeats (SSRs) from Japanese bunching onion, and 1 SSR from bulb onion (A. cepa) – on 15 linkage groups covering 947 centiMorgans (cM). The linkage map of P₂ was constructed with the (P₁)BC₁ population and composed of 120 loci – 105 AFLPs, 1 CAPS, and 13 SSRs developed from Japanese bunching onion and 1 SSR from bulb onion – on 14 linkage groups covering 775 cM. Both maps were not saturated but were considered to cover the majority of the genome. Nine linkage groups in P₂ map were connected with their counterparts in P₁ map using co-dominant anchor markers, 13 SSRs and 1 CAPS.     

SSR marker tightly linked to the Ti locus in Soybean [Glycine max (L.) Merr.]

Soybean is a major source of protein meal in the world. Soybean kunitz trypsin inhibitor (SKTI) protein is a responsible for the inferior nutritional quality of unheated or incompletely heated soybean meal. The primary objective of this research was to identify DNA markers linked to the Ti locus controlling presence and absence of kunitz trypsin inhibitor protein. Two mapping populations were developed. Population 1 was derived from a cross between cultivar Jinpumkong2 (TiTi) and C242 (titi). Population 2 was made from a mating between cultivar Clark (TiTi) and C242. The F₁ plants were grown in the greenhouse to produce F₂ seeds. Each F₂ seed from F₁ plants was analyzed electrophoretically to determine the presence of the SKTI protein band. One-thousand RAPD primers, 342 AFLP primer sets, and 35 SSR primers were used to map Ti locus in population 1 and 2. The presence of SKTI protein was dominant to the lack of a SKTI protein and kunitz trypsin inhibit protein band was controlled by a single locus. Twelve DNA markers (4 RAPD, 4 AFLP, and 3 SSR) and Ti locus were found to be genetically linked in population 1 consisted with 94 F₂ individual plants. Three SSR markers (Satt409, Satt228, and Satt429) were linked with Ti locus within 10 cM. Satt228 marker was tightly linked with Ti locus. Satt228 marker was tightly linked within 0–3.7 cM of the Ti locus and may be useful in a marker assisted selection program.     

Chromosomal assignment of AFLP markers in upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.)

In this research, we used two sets of cotton aneuploid (G. hirsutum × G. tomentosum and G. hirsutum × G. barbadense) plants to locate AFLP markers to chromosomes using deletion analysis method. Thirty-eight primer combinations were used to generate 608 polymorphic AFLP markers. A total of 98 AFLP markers were assigned to 22 different cotton chromosomes or chromosome arms. Of those assigned markers, 63.3% were assigned to A genome and 36.7% were assigned to D genome. A low rate (14.3%) of common markers were found between those assigned AFLP markers with the AFLP markers from an intraspecific cross population developed previous in our lab. Based on the 16 common markers, we were able to associate the 13 linkage groups previously identified in our lab to eight chromosomes. Further research will be carried out by using SSR markers with known location to associate unassigned linkage groups to chromosomes.     

RAPD and SCAR markers for resistance to acochyta blight in lentil

Resistance to ascochyta blight of lentil (Lens culinaris Medikus),caused by the fungus Ascochyta lentis, is determined by a single recessive gene, ral ₂, in the lentil cultivar Indian head. Sixty F₂ individuals from a cross between Eston (susceptible) and Indian head (resistant) lentil were analyzed for the presence of random amplified polymorphic DNA (RAPD) markers linked to the ral ₂gene, using bulked segregant analysis (BSA). Out of 800 decanucleotide primers screened, two produced polymorphic markers that co-segregated with the resistance locus. These two RAPD markers, UBC227₁₂₉₀and OPD-10₈₇₀, flanked and were linked in repulsion phase to the gene ral ₂ at 12 cm and 16 cm, respectively. The RAPD fragments were converted to SCAR markers. The SCAR marker developed from UBC227₁₂₉₀ could not detect any polymorphism between the two parents or in the F₂. The SCAR marker developed from OPD-10₈₇₀ retained its polymorphism. The polymorphic RAPD marker UBC227₁₂₉₀ and the SCAR marker developed from OPD-10₈₇₀ can be used together in a marker assisted selection program for ascochyta blight resistance in lentil. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of microsatellite markers linked to the blast resistance gene <Emphasis Type="Italic">Pi-1(t)</Emphasis> in rice

The present work was conducted to identify microsatellite markers linked to the rice blast resistance gene Pi-1(t) for a marker-assisted selection program. Twenty-four primer pairs corresponding to 19 microsatellite loci were selected from the Gramene database (www. gramene.org) considering their relative proximity to Pi-1(t) gene in the current rice genetic map. Progenitors and DNA bulks of resistant and susceptible families from F₃ segregating populations of a cross between the near-isogenic lines C101LAC (resistant) and C101A51 (susceptible) were used to identify polymorphic microsatellite markers associated to this gene through bulked segregant analysis. Putative molecular markers linked to the blast resistance gene Pi-1(t) were then used on the whole progeny for linkage analysis. Additionally, the diagnostic potential of the microsatellite markers associated to the resistance gene was also evaluated on 17 rice varieties planted in Latin America by amplification of the specific resistant alleles for the gene in each genotype. Comparing with greenhouse phenotypic evaluations for blast resistance, the usefulness of the highly linked microsatellite markers to identify resistant rice genotypes was evaluated. As expected, the phenotypic segregation in the F₃ generation agreed to the expected segregation ratio for a single gene model. Of the 24 microsatellite sequences tested, six resulted polymorphic and linked to the gene. Two markers (RM1233*I and RM224) mapped in the same position (0.0 cM) with the Pi-1(t) gene. Other three markers corresponding to the same genetic locus were located at 18.5 cM above the resistance gene, while another marker was positioned at 23.8 cM below the gene. Microsatellite analysis on elite rice varieties with different genetic background showed that all known sources of blast resistance included in this study carry the specific Pi-1(t) allele. Results are discussed considering the potential utility of the microsatellite markers found, for MAS in rice breeding programs aiming at developing rice varieties with durable blast resistance based on a combination of resistance genes. Centro Internactional de Agricultura Tropical (CIAT) institute where the research was carried out     

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.     

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.     

Development and characterization of tomato SSR markers from genomic sequences of anchored BAC clones on chromosome 6

Simple sequence repeat motifs are abundant in plant genomes and are commonly used molecular markers in plant breeding. In tomato, currently available genetic maps possess a limited number of simple sequence repeat (SSR) markers that are not evenly distributed in the genome. This situation warrants the need for more SSRs in genomic regions lacking adequate markers. The objective of the study was to develop SSR markers pertaining to chromosome 6 from bacterial artificial chromosome (BAC) sequences available at Solanaceae Genomics Network. A total of 54 SSR primer pairs from 17 BAC clones on chromosome 6 were designed and validated. Polymorphism of these loci was evaluated in a panel of 16 genotypes comprising of Solanum lycopersicum and its wild relatives. Genetic diversity analysis based on these markers could distinguish genotypes at species level. Twenty-one SSR markers derived from 13 BAC clones were polymorphic between two closely related tomato accessions, West Virginia 700 and Hawaii 7996 and were mapped using a recombinant inbred line population derived from a cross between these two accessions. The markers were distributed throughout the chromosome spanning a total length of 117.6 cM following the order of the original BAC clones. A major QTL associated with resistance to bacterial wilt was mapped on chromosome 6 at similar location of the reported Bwr-6 locus. These chromosome 6-specific SSR markers developed in this study are useful tools for cultivar identification, genetic diversity analysis and genetic mapping in tomato.