Partial Linkage Map Research Articles

QTL analysis for low temperature tolerance of wild potato species Solanum commersonii in natural field trials

Potato cultivars (Solanum tuberosum L.) are delicate to cold and frost. Low temperatures have a negative impact on potato growth, development and yield. However, genetic detection of frost tolerance loci is currently lacking. Here, we report a BC1 population that was constructed by crossing the diploid cold-resistant wild species S. commersonii with the diploid cold-sensitive wild species S. verrucosum. The frost tolerance of the resulting offspring was determined through four years of natural field frost experiments. Together with bulked segregant analysis (BSA) technology and traditional quantitative trait locus (QTL) mapping, four highly related QTLs were detected on Chr02 and Chr11. Furthermore, we constructed a partial genetic linkage map of Chr02, and two QTLs (QTL1 and QTL2) were detected on Chr02. Four genes located in candidate intervals have been reported to be associated with tolerance to abiotic stress and were significantly differentially expressed among the resistant and sensitive. Taken together, our results also suggest that the frost resistance of plants under variable low-temperature conditions is controlled by different loci.

Localization of TWISTED NEEDLES Locus on Linkage Map of Japanese Cedar (Cryptomeria japonica D. Don)

Sugi (Cryptomeria japonica D. Don) is an important forestry species in Japan. C. japonica ‘Spiralis’ is a mutant with twisted needles. The mutant is called Yore-sugi in Japan and is known as ‘Rasen’ in other countries. The twisted trait is regulated by a dominant gene called TWISTED NEEDLES, and it can be identified by observing the needles within 1 to 2 months after germination. The TWISTED NEEDLES gene may be useful for improving the efficiency of genome editing technology in C. japonica. In this study, we attempted to identify the linkage group of the TWISTED NEEDLES locus and investigate markers that sandwich this locus using the mapping family. First, we identified the linkage group containing the TWISTED NEEDLES locus based on the distortion from the expected segregation ratio using 32 mutant individuals of the mapping family. The segregation distortion showed that the TWISTED NEEDLES locus was located on the 11th linkage group (LG11). Next, a linkage map of LG11 was constructed based on genotype data from the single-nucleotide polymorphism (SNP) markers and double digested restriction site-associated DNA sequencing (ddRAD-seq) using 123 individuals of the MMY-1 family. On this map, six markers were located at the same position as the TWISTED NEEDLES locus. To investigate markers sandwiching the TWISTED NEEDLES locus, a partial linkage map around the TWISTED NEEDLES locus was constructed using 643 individuals of the MMY-1 family. The TWISTED NEEDLES locus was located in the 0.6 cM region between gSNP01822 and the other five markers (Contig_4705-179, Contig_4518-93, Contig_4398-118, gSNP04056, and Contig_4970-113).

Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin.

The hull-less pumpkin (Cucurbita pepo) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F2 and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F2:3 progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F2 (n = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (Cphl-1). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the C. pepo hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The Cphl-1-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors viz., “NAC” (Cp4.1LG12g04350) and “MYB” (Cp4.1LG12g03120). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.

Mapping QTL for important seed traits in an interspecific F2 population of pigeonpea

Seed traits present important breeding targets for enhancing grain yield and quality in various grain legume crops including pigeonpea. The present study reports significant genetic variation for six seed traits including seed length (SL), seed width (SW), seed thickness (ST), seed weight (SWT), electrical conductivity (EC) and water uptake (WU) among Cajanus cajan (L.) Millspaugh acc. ICPL 20340 and Cajanus scarabaeoides (L.) Thouars acc. ICP 15739 and an F2 population derived from this interspecific cross. Maximum phenotypic values recorded for the F2 population were higher than observed in the parent ICPL 20340 [F2 max vs ICPL 20340: SW (7.05 vs 5.38), ST (4.63 vs 4.51), EC (65.17 vs 9.72), WU (213.17 vs 109.5)], which suggested contribution of positive alleles from the wild parent, ICP 15739. Concurrently, to identify the QTL controlling these seed traits, we assayed two parents and 94 F2 individuals with 113 polymorphic simple sequence repeat (SSR) markers. In the F2 population, 98 of the 113 SSRs showed Mendelian segregation ratio 1:2:1, whereas significant deviations were observed for 15 SSRs with their χ 2 values ranging between 6.26 and 20.62. A partial genetic linkage map comprising 83 SSR loci was constructed. QTL analysis identified 15 marker-trait associations (MTAs) for seed traits on four linkage groups i.e. LG01, LG02, LG04 and LG05. Phenotypic variations (PVs) explained by these QTL ranged from 4.4 (WU) to 19.91% (EC). These genomic regions contributing significantly towards observed variability of seed traits would serve as potential candidates for future research that aims to improve seed traits in pigeonpea.

Genetic mapping of the three-pistil gene Pis1 in an F2 population derived from a synthetic hexaploid wheat using multiple molecular marker systems

The wheat spike mutant 'three-pistil' (TP) exhibits normal external morphology but produces two additional pistils per floret. Much attention has been paid to this natural mutation because elucidation of its genetic foundation potentially paves a way to increase the number of grains per spike for breeding. Our previous studies roughly mapped the causal locus of TP on chromosome 2D. In this study, we performed genetic mapping of the three-pistil gene Pis1 in an F2 population derived from a cross of TP and synthetic hexaploid wheat of which chromosome 2D was from Aegilops tauschii. Segregation analysis in the F2 population confirmed the dominance of the Pis1 locus. Bulked segregant analysis with three DNA marker systems revealed a total of 18 markers genetically linked with Pis1. Successive genetic linkage analysis of the F2 individuals using the 18 markers identified two sequence-related amplified polymorphisms markers, Me5-eM33 and Me26-eM33, flanked the Pis1 locus at distances of 0.6 and 1.7 cM, respectively. Integration of the genetic linkage and previously discovered DNA markers associated with Pis1 revealed a potential location of the Pis1 locus between Me5-eM33 and a KASP marker M75. Thus, the constructed partial genetic linkage map is useful for the isolation of Pis1 and marker-assisted breeding in wheat.

Marker-Assisted Selection of Trees with MALE STERILITY 1 in Cryptomeria japonica D. Don

The practical use of marker-assisted selection (MAS) is limited in conifers because of the difficulty with developing markers due to a rapid decrease in linkage disequilibrium, the limited genomic information available, and the diverse genetic backgrounds among the breeding material collections. First, in this study, two families were produced by artificial crossing between two male-sterile trees, ‘Shindai11’ and ‘Shindai12’, and a plus tree, ‘Suzu-2’ (Ms1/ms1) (S11-S and S12-S families, respectively). The segregation ratio between the male-sterile and male-fertile trees did not deviate significantly from the expected 1:1 ratio in either family. These results clearly suggested that the male-sterile gene of ‘Shindai11’ and ‘Shindai12’ is MALE STERILITY 1 (MS1). Since it is difficult to understand the relative positions of each marker, due to the lack of a linkage map which all the closely linked markers previously reported are mapped on, we constructed a partial linkage map of the region encompassing MS1 using the S11-S and S12-S families. For the S11-S and S12-S families, 19 and 18 markers were mapped onto the partial linkage maps of the MS1 region, respectively. There was collinearity (conserved gene order) between the two partial linkage maps. Two markers (CJt020762_ms1-1 and reCj19250_2335) were mapped to the same position as the MS1 locus on both maps. Of these markers, we used CJt020762 for the MAS in this study. According to the MAS results for 650 trees from six prefectures of Japan (603 trees from breeding materials and 47 trees from the Ishinomaki natural population), five trees in Niigata Prefecture and one tree in Yamagata Prefecture had heterozygous ms1-1, and three trees in Miyagi Prefecture had heterozygous ms1-2. The results obtained in this study suggested that ms1-1 and ms1-2 have different geographical distributions. Since MAS can be used effectively to reduce the labor and time required for selection of trees with a male-sterile gene, the research should help ensure that the quantity of breeding materials will increase to assist future tree-breeding efforts.

Confirmation of the effectiveness and genetic positions of disease resistance loci in ‘Kishmish Vatkana’ (Ren1) and ‘Villard Blanc’ (Ren3 and Rpv3)

This study aimed to validate the effectiveness and to genetically characterise the fungal disease resistance genes of ‘Kishmish Vatkana’ and ‘Villard Blanc’ in South Africa using microsatellite (SSR) markers and a Quantitative Trait Loci (QTL) approach. An F1 ‘Sunred Seedless’ × ‘Kishmish Vatkana’ cross was used to generate a partial linkage map for chromosome 13 known to harbour the Ren1 powdery mildew locus of ‘Kishmish Vatkana’. The effectiveness of this locus was validated, explaining between 44.8% and 57.7% of the observed phenotypic variance. An F1 ‘Villard Blanc’ × ‘G1-6604’ cross was used to generate partial linkage maps for chromosomes 15 and 18, reported to harbour fungal resistance genes of ‘Villard Blanc’. The powdery mildew QTL (Ren3) was validated on chromosome 15 of ‘Villard Blanc’, which explained between 18.9% and 23.9% of the phenotypic variance observed. The downy mildew resistance QTL on chromosome 18 (Rpv3) of ‘Villard Blanc’ was also confirmed, and it explained between 19.1% and 21.2% of the phenotypic variance observed. This molecular information and individual sources of resistance have already been implemented in the marker-assisted selection (MAS) and gene pyramiding efforts of the table grape breeding program of the Agricultural Research Council (ARC) Infruitec-Nietvoorbij.

Characterisation and mapping of adult plant stripe rust resistance in wheat accession Aus27284

A new adult plant stripe rust resistance gene, Yr80, was identified in a common wheat landrace Aus27284. Linked markers were developed and validated for their utility in marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most important constraints to global wheat production. The identification and characterisation of new sources of host plant resistance enrich the gene pool and underpin deployment of resistance gene pyramids in new cultivars. Aus27284 exhibited resistance at the adult plant stage against predominant Pst pathotypes and was crossed with a susceptible genotype Avocet S. A recombinant inbred line (RIL) population comprising 121 lines was developed and tested in the field at three locations in 2016 and two in 2017 crop seasons. Monogenic segregation for adult plant stripe rust response was observed among the Aus27284/Avocet S RIL population and the underlying locus was temporarily designated YrAW11. Bulked-segregant analysis using the Infinium iSelect 90K SNP wheat array placed YrAW11 in chromosome 3B. Kompetitive allele specific PCR (KASP) primers were designed for the linked SNPs and YrAW11 was flanked by KASP_65624 and KASP_53292 (3cM) proximally and KASP_53113 (4.9cM) distally. A partial linkage map of the genomic region carrying YrAW11 comprised nine KASP and two SSR markers. The physical position of KASP markers in the pseudomolecule of chromosome 3B placed YrAW11 in the long arm and the location of markers gwm108 and gwm376 in the deletion bin 3BL2-0.22 supported this conclusion. As no other stripe rust resistance locus has been reported in chromosome 3BL, YrAW11 was formally designated Yr80. Marker KASP_ 53113 was polymorphic among 94% of 81 Australianwheat cultivars used for validation.

Mapping the glaucousness suppressor Iw1 from wild emmer wheat “PI 481521”

Many species of Triticeae display a glaucous phenotype. In wheat, glaucousness/waxiness on spikes, leaves and shoots is controlled by wax production genes (W loci) and epistatic inhibitors (Iw loci). In this study, a suppressor of glaucousness from wild emmer wheat (Triticum turgidum ssp. dicoccoides) accession “PI 481521” was investigated in a pair of durum (T. turgidum ssp. durum cv. “Langdon”, LDN)—wild emmer wheat chromosome substitution lines, LDN and “LDNDIC521-2B”. Genetic analysis revealed that the non-glaucous phenotype of LDNDIC521-2B was controlled by the dominant glaucous suppressor Iw1 on the short arm of chromosome 2B. In total, 371 2B-specific marker differences were identified between LDN and LDNDIC521-2B. The location of the Iw1 gene was mapped using an F2 population that stemmed from LDN and LDNDIC521-2B, generating a partial linkage map that included 19 simple sequence repeats (SSR) and ten gene-based markers. On the current map, the Iw1 gene was located within the Xgwm614–BE498111 interval, and cosegregated with BQ788707, CD893659, CD927782, CD938589, and Xbarc35. Mapping of Iw1 in LDNDIC521-2B, a publically accessible and widely distributed line, will provide valuable information for marker-assisted selection of the agronomically important trait of glaucousness.

Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination

Background: Short-stature cultivars have been developed by breeders worldwide to reduce lodging and increase grain yield. In barley, the effort to achieve short stature genotypes has relied in part on the sdw1 / denso gene. In the present study populations, representing different rounds of recombination were used for the analysis of phenotypic effects associated with the sdw1 / denso locus. Other studies have mostly focused only on one type of population. Many different QTLs mapped at the same position as the sdw1/denso locus may indicate a pleiotropy of this gene or a tight linkage between genes conditioning quantitative traits. To date, results of studies have not unequivocally proven either of these two phenomena. Results: In this study, both breeding and molecular mapping experiments were undertaken to examine 200 single seed descent (SSD) and 60 doubled haploid (DH) lines obtained from the Maresi (with a semi-dwarfing gene) and Pomo cross combination. These lines and their parental forms were evaluated for the type of juvenile growth habit and certain agronomic traits were measured after harvesting. The estimates of mean values, standard errors and significance of effects were analyzed. In terms of the analyzed characteristics, the greatest variability was obtained for genotypes with the prostrate growth habit. Microsatellite markers (SSR) were also used to identify co-segregation with the sdw1/denso locus and Bmag0013, Bmag0877, Bmag0306b markers were linked the closest. A partial linkage map of chromosome 3H with the sdw1/denso semi-dwarfing gene was constructed and QTLs were identified. Conclusions: Our experiments confirmed the impact of the semi-dwarfing gene on plant height, heading and flowering date both in SSD and DH populations, which may indicate pleiotropy. On the other hand, a partial linkage between sdw1 / denso locus and grain weight per spike and 1000-grain weight was found in the SSD population. A combination of a biometric approach with molecular analyses of different populations may present the opportunity to solve the problem of the distinction between the pleiotropic effects of semi-dwarfing genes and linkage effects. Normal 0 21 false false false ES X-NONE X-NONE

Detection of downy and powdery mildew resistance QTL in a ‘Regent’ × ‘RedGlobe’ population

AbstractOne hundred and eighty six F1plants from a ‘Regent’ × ‘RedGlobe’ cross were used to generate a partial linkage map with 139 microsatellite markers spanning all 19 chromosomes. Phenotypic scores for downy mildew, taken over two years, confirmed a major resistance QTL (Rpv3) against downy mildew in the interval VVIN16-cjvh to UDV108 on chromosome 18 of ‘Regent’. This locus explained up to 62 % of the phenotypic variance observed. Additionally a putative minor downy mildew resistance locus was observed on chromosome 1 in one season. A major resistance locus against powdery mildew (Ren3) was also identified on chromosome 15 of ‘Regent’ in the interval UDV116 to VChr15CenGen06. This study established the efficacy of and validated the ‘Regent’-derived downy and powdery mildew major resistance genes/QTL under South African conditions. Closely linked SSR markers for marker-assisted selection and gene pyramiding strategies were identified.

Molecular mapping of three nuclear male sterility mutant genes in cultivated sunflower (Helianthus annuus L.)

The nuclear male sterility (NMS) trait is a useful tool for sunflower (Helianthus annuus L.) breeding and genetic programs. Previously, we induced NMS mutants in cultivated line HA 89. The mutants possessed single recessive genes ms6, ms7, and ms8, respectively, in NMS HA 89-872, NMS HA 89-552, and NMS HA 89-747. Bulked segregant analysis based on the male-fertile and male-sterile DNA pools and 560 simple sequence repeat and insertion/deletion markers randomly selected from 17 linkage groups (LGs) were used to locate ms6 to LG16, ms7 to LG6, and ms8 to LG5. Subsequent genotyping of three F2 populations of 88, 93, and 76 individuals confirmed their map positions. Additional polymorphic markers derived from four restriction fragment length polymorphism-converted sequence-tagged site primer pairs were identified. A partial linkage map consisting of eight markers was constructed for the ms6 locus, covering a region of 69.24 cM, with markers ORS807 and ORS996 flanking the ms6 locus at distances of 7.2 and 18.5 cM, respectively. Six markers were constructed for ms7, covering a region of 53.4 cM, with ORS608 and ORS1229 flanking ms7 at distances of 2.6 and 9.5 cM, respectively. Ten markers were constructed for ms8, covering a region of 18.0 cM, with six markers below ms8 and CRT518 above flanking ms8 at distances of 7.4 and 3.8 cM, respectively. The markers and mapping information will be useful for selection of the recessive NMS genes in sunflower breeding programs.

Genetic effects of dwarfing gene Rht-5 on agronomic traits in common wheat (Triticum aestivum L.) and QTL analysis on its linked traits

In order to evaluate the genetic effects of Rht-5 dwarfing gene on agronomic traits in common wheat, F2 population and 32 F2:3 lines derived from the cross between Jinmai47 (rht-5) and Marfed M (Rht-5) along with the two parents were grown in the winter wheat growing seasons of 2011–2012 and 2012–2013, respectively. The F2 population formed the mapping population and their phenotypic and genotypic data were merged for QTL mapping. The dwarf and tall individuals in the F2 population were selected to compose the F2:3 lines. Analysis of variance in the F2 population and F2:3 lines showed highly significant differences among individuals or lines for all of traits studied, except for biomass and grain yield. In general, in the background of Jinmai47, dwarfing gene Rht-5 was associated with a plant height reduction of 25.84%, delaying heading date by 1 day, increasing the number of fertile tillers plant−1 by 37.39%, while reducing the number of spikelets spike−1 and number of grains spike−1 by 8.07% and 22.31%, respectively. Individuals with earlier heading date, longer spikes, more spikelets spike−1, and more grains spike−1 could be observed in the dwarf lines when compared to the dwarf parent. Plant height showed highly positive and significant correlation with peduncle length (0.88), spike length (0.80), number of spikelets spike−1 (0.63), number of grains spike−1 (0.64), biomass (0.47), grain yield (0.56) and harvest index (0.37), whereas it had negative and highly significant correlation with the number of fertile tillers plant−1 (−0.64). A partial chromosomal linkage map was constructed with three polymorphic markers based on their genotypes in the F2 population. Using composite interval mapping (CIM) analysis, four QTLs were detected for plant height, heading date, peduncle length and number of grains spike−1 and accounted for up to 11.82%, 8.02%, 10.32% and 15.65% of the phenotypic variation, respectively. The results of the current study could be useful for proper use of Rht-5 dwarfing gene in breeding programs to improve lodging tolerance, yield potential in wheat and increase efficiency of marker assisted selection for agronomic traits.

Establishment of a microsatellite panel covering the sugi (Cryptomeria japonica) genome, and its application for localization of a male-sterile gene (ms-2)

A microsatellite (simple sequence repeat; SSR) panel for Cryptomeria japonica was established, using both newly developed and previously reported markers, to construct a frame of linkage map and facilitate localization of important genes in this species. In this study, 32 new expressed sequence tag SSRs (EST-SSRs) and 12 new genomic SSRs (gSSRs) were developed. Their average polymorphism information content (PIC) values were 0.549 and 0.776, respectively. The markers were mapped onto a high-density linkage map. The SSR panel that was established to cover the genome consisted of 46 gSSRs and 47 EST-SSRs. The number of SSR markers in each linkage group, the average map distance between loci within a linkage group, and the average PIC values in each linkage group ranged from 6 to 13, 6.77 to 19.88 and 0.475 to 0.712, respectively. The utility of the SSR panel was tested by using it to localize a male-sterile gene, ms-2. The ms-2 locus was successfully localized on the linkage group 5 using 33 SSR markers (three SSRs per linkage group) which were selected from the SSR panel based on the existence of polymorphisms and the absence of null alleles in the mapping population for ms-2. A partial linkage map surrounding the ms-2 locus was then constructed using a further 57 single nucleotide polymorphisms and three SSRs, to facilitate future development of markers tightly linked to the ms-2 locus for use in marker-assisted selection. The SSR panel covering the C. japonica genome will allow researchers to localize important genes efficiently.

The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don.

BackgroundHigh-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS). MAS is quite challenging in conifers because of their large, complex, and poorly-characterized genomes. Our goal was to construct a high-density linkage map to facilitate the identification of markers that are tightly linked to a major recessive male-sterile gene (ms1) for MAS in C. japonica, a species that is important in Japanese afforestation but which causes serious social pollinosis problems.ResultsWe constructed a high-density saturated genetic linkage map for C. japonica using expressed sequence-derived co-dominant single nucleotide polymorphism (SNP) markers, most of which were genotyped using the GoldenGate genotyping assay. A total of 1261 markers were assigned to 11 linkage groups with an observed map length of 1405.2 cM and a mean distance between two adjacent markers of 1.1 cM; the number of linkage groups matched the basic chromosome number in C. japonica. Using this map, we located ms1 on the 9th linkage group and constructed a partial linkage map around the ms1 locus. This enabled us to identify a marker (hrmSNP970_sf) that is closely linked to the ms1 gene, being separated from it by only 0.5 cM.ConclusionsUsing the high-density map, we located the ms1 gene on the 9th linkage group and constructed a partial linkage map around the ms1 locus. The map distance between the ms1 gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the ms1 gene will facilitate the early selection of male-sterile trees, which should expedite C. japonica breeding programs aimed at alleviating pollinosis problems without harming productivity.

Identification of quantitative trait loci for protein content, oil content and oil quality for groundnut ( Arachis hypogaea L.)

Very few efforts have been made to improve the nutritional quality of groundnut, as biochemical estimation of quality traits is laborious and uneconomic; hence, it is difficult to improve them through traditional breeding alone. Identification of molecular markers for quality traits will have a great impact in molecular breeding. An attempt was made to identify microsatellite or simple sequence repeat (SSR) markers for important nutritional traits (protein content, oil content and oil quality in terms of oleic acid, linoleic acid and oleic/linoleic acid ratio) in a mapping population consisting of 146 recombinant inbreed lines (RILs) of a cross TG26 × GPBD4. Phenotyping data analysis for quality traits showed significant variation in the population and environment, genotype × environment interaction and high heritability was observed for all the traits. Negative correlation between protein content and oil content, oleic acid and linoleic acid indicated their antagonistic nature. After screening >1000 SSR markers, a partial genetic linkage map comprising of 45 SSR loci on 8 linkage groups with an average inter-marker distance of 14.62 cM was developed. QTL analysis based on single marker analysis (SMA) and composite interval mapping identified some candidate SSR markers associated with major QTLs as well as several minor QTLs for the nutritional traits. Validation of these major QTLs using a wider genetic background may provide the markers for molecular breeding for improving groundnut for nutritional traits.

Mapping QTLs for Male Sterile Gene in YM-Type Thermo-Sensitive Male Sterile Line of Wheat

The sterile gene of YM-type thermo-sensitive male sterile wheat ( Triticum aestivum L.) line has been mapped on chromosome arm 1BS, which was more than 10 cM distant from the adjacent molecular markers. For detecting markers with short distances to this gene, a population with 200 F 2 plants was constructed from the cross between ATM3314 and the restorer line Chinese Spring. Among 20 simple sequence repeat (SSR) markers distributing evenly on 1BS, 5 SSRs showed polymorphism between the parents and between the male sterile and fertile bulks. A 1BS partial linkage map carrying the 5 markers was obtained and QTLs for the male sterility were identified using composite interval mapping method. One major QTL and one minor QTL were detected and designated rfv1-1 and rfv1-2, respectively. QTL rfv1-1 (LOD = 8.80) was located between markers Xgwm18 and Xwmc406 with the genetic distances of 6.0 cM and 4.6 cM to the adjacent markers, respectively. On this locus, the additive and dominant effects were 23.87 and 10.44, respectively, which accounted for 23.9% of the phenotypic variation. QTL rfv1-2 (LOD = 3.10) was mapped between markers Xwmc406 and Xbarc8 with the genetic distances of 4.0 cM and 3.4 cM, respectively. This locus had additive effect of 17.59 and dominant effect of 5.99, and explained 7.8% of the phenotypic variation. These results are propitious for fine mapping and positional cloning of this male sterile gene.

Detection and fine mapping of quantitative trait loci for bone traits on chicken chromosome one

In broiler chickens, bone problems are an important welfare issue that has been linked to genetic selection for rapid growth. The objectives of this study were to identify and fine map quantitative trait loci (QTL) associated with bone traits. The Northeast Agricultural University resource population (NEAURP) being an F(2) population was used in this study, and a total of 17 bone traits were measured. In primary genome scan, the linkage map was constructed with 23 microsatellite markers across the entire chicken chromosome 1. Seventeen QTLs for bone traits were identified and 12 of these were found between LEI0079 and ROS0025 (50.8 cM apart). To fine map the QTLs located between LEI0079 and ROS0025, more markers and more individuals were used and a new partial linkage map was constructed. The confidence intervals for QTLs were sharply narrowed down from 24.5∼52.6 to 2.7∼17.0 Mb. This study identified chromosome regions harbouring significant QTLs affecting bone traits and showed that the use of more markers and individuals could decrease the confidence interval of QTL effectively. The results provide a useful reference for further candidate gene research and MAS for bone traits.

Identification of Flanking Markers for the Stem Rust Resistance Gene Sr6 in Wheat

ABSTRACTThe wheat (Triticum aestivum L. and T. turgidum L.) stem rust resistance gene Sr6 confers a high level of resistance against a wide range of races of Puccinia graminis Pers.:Pers. f. sp. tritici Eriks. and E. Henn. in North America. In this study, we report the identification of flanking markers for Sr6. We used a population of 139 recombinant inbred lines from the cross MN99394 × MN98550. A partial linkage map of chromosome 2D comprised Xgwm484, Xcfd77, Xcfd43, Xwmc453, Sr6, XwPt_4381, XwPt_0330, Xgpw94049, and Xgwm102. Four markers mapped distal to Sr6, while the other four were proximal within distances of 4.8 and 6.5 cM, respectively. Marker‐assisted selection and pyramiding of Sr6 with other stem rust resistance genes could benefit from the availability of Sr6‐flanking markers.

A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.)

Late leaf spot (LLS) and rust are two major foliar diseases of groundnut (Arachis hypogaea L.) that often occur together leading to 50–70% yield loss in the crop. A total of 268 recombinant inbred lines of a mapping population TAG 24 × GPBD 4 segregating for LLS and rust were used to undertake quantitative trait locus (QTL) analysis. Phenotyping of the population was carried out under artificial disease epiphytotics. Positive correlations between different stages, high to very high heritability and independent nature of inheritance between both the diseases were observed. Parental genotypes were screened with 1,089 simple sequence repeat (SSR) markers, of which 67 (6.15%) were found polymorphic. Segregation data obtained for these markers facilitated development of partial linkage map (14 linkage groups) with 56 SSR loci. Composite interval mapping (CIM) undertaken on genotyping and phenotyping data yielded 11 QTLs for LLS (explaining 1.70–6.50% phenotypic variation) in three environments and 12 QTLs for rust (explaining 1.70–55.20% phenotypic variation). Interestingly a major QTL associated with rust (QTLrust01), contributing 6.90–55.20% variation, was identified by both CIM and single marker analysis (SMA). A candidate SSR marker (IPAHM 103) linked with this QTL was validated using a wide range of resistant/susceptible breeding lines as well as progeny lines of another mapping population (TG 26 × GPBD 4). Therefore, this marker should be useful for introgressing the major QTL for rust in desired lines/varieties of groundnut through marker-assisted backcrossing.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-010-1366-x) contains supplementary material, which is available to authorized users.