Average Interval Distance Research Articles

High-density genetic map construction and QTL mapping of a zigzag-shaped stem trait in tea plant (Camellia sinensis)

The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0.68 cM. A quantitative trait locus (QTL) for the zigzag-shaped trait was identified on chromosome 4, within a 61.2 to 97.2 Mb range, accounting for a phenotypic variation explained (PVE) value of 13.62%. Within this QTL, six candidate genes were pinpointed. To better understand their roles, we analyzed gene expression in various tissues and individuals with erect and zigzag-shaped stems. The results implicated CsXTH (CSS0035625) and CsCIPK14 (CSS0044366) as potential key contributors to the zigzag-shaped stem formation. These discoveries lay a robust foundation for future functional genetic mapping and tea plant genetic enhancement.

Construction of Genetic Linkage Map and Mapping QTL Specific to Leaf Anthocyanin Colouration in Mapping Population 'Allahabad Safeda' × 'Purple Guava (Local)' of Guava (Psidium guajava L.).

In the present investigation, F1 hybrids were developed in guava (Psidium guajava L.) by crossing high leaf-anthocyanin reflective-index (ARI1) content cultivars purple guava (local) ‘PG’, ‘CISH G-1’ and low leaf-ARI1 content cultivar Seedless ‘SL’ with Allahabad Safeda ‘AS’. On the basis of phenotypic observations, high ARI1 content was observed in the cross ‘AS’ × ‘PG’ (0.214). Further, an SSR-markers-based genetic linkage map was developed from a mapping population of 238 F1 individuals derived from cross ‘AS’ × ‘PG’. The linkage map comprised 11 linkage groups (LGs), spanning 1601.7 cM with an average marker interval distance of 29.61 cM between adjacent markers. Five anthocyanin-content related gene-specific markers from apple were tested for parental polymorphism in the genotypes ‘AS’ and ‘PG’. Subsequently, a marker, viz., ‘MdMYB10F1′, revealed a strong association with leaf anthocyanin content in the guava mapping population. QTL (qARI-6-1) on LG6 explains much of the variation (PVE = 11.51% with LOD = 4.67) in levels of leaf anthocyanin colouration. This is the first report of amplification/utilization of apple anthocyanin-related genes in guava. The genotypic data generated from the genetic map can be further exploited in future for the enrichment of linkage maps and for identification of complex quantitative trait loci (QTLs) governing economically important fruit quality traits in guava.

High-density genetic mapping identified a major locus for environmental sex expression in pumpkin (Cucurbita moschata Duch.)

Long-day length and high temperature inhibit sex expression in pumpkin (Cucurbita moschata Duch.), and therefore directly impact the production potential. In this study, female flowering patterns in photoperiod-insensitive (PPIS) and photoperiod-sensitive (PPS) germplasms differed significantly in a moderately long day and high temperature environment. However, both germplasms exhibited a similar response in short day with either low temperature or high temperature environment. Photoperiod sensitivity led to this difference in sex expression between the germplasms. For the traits of 1st female flowering node (FFFN) and number of female flowers (NFF), high-density linkage map construction and quantitative trait locus (QTL) mapping were performed using SLAF-seq technology and 162 F2 individuals generated from PPIS and PPS. In total, 4 655 SLAFs were selected and mapped on 20 linkage groups (LGs). The total map length was 2 502.01 cM with an average interval distance of 0.75 cM. Major QTLs for both FFFN and NFF were detected on LG6 with intervals of 7.89 and 17.67 cM and PVE values of 30.5% and 22.9%, respectively. Further analyses of the major locus for FFFN revealed 73 protein-coding genes. Among them, 4 were related to sex expression, photoperiod flowering, and hormone response. An InDel (insertion and deletion) marker partially correlated with FFFN of the F2 population was also developed. Our study identified the QTL for the sex expression response to environmental factors using the high-density linkage map. The identified candidate genes and markers will provide useful information about the molecular interaction between the environment and sex expression and for marker-assisted selection of pumpkin environment-insensitive resources.

Identification of rice blast resistance candidate genes based on integrating Meta-QTL and RNA-seq analysis

<p id="C3"><italic>Magnaporthe oryzae</italic> seriously devastates rice production, and resistant cultivars can lose resistance within a few years due to the pathogenic variability of <italic>M. oryzae.</italic> Therefore, it is essential to explore continuously novel blast-resistance genes for breeding broad-spectrum resistance cultivars. In this study, firstly, 50 Meta-QTLs (including at least 2 original QTLs) were identified on 12 chromosomes by meta-analysis of blast-resistance 783 QTLs from 43 literatures. The average interval distance was 0.87 Mb in these Meta-QTLs, which contained a total of 4718 interval genes. Subsequently, based on integrated analysis of blast-resistance Meta-QTLs and RNA-seq, the result identified 2193 common genes which were not only located on blast-resistance Meta-QTLs, but also significantly differentially expressed in response to the <italic>M. oryzae</italic>. Among them, 22 cloned genes had been reported to be involved in defense responses to <italic>M. oryzae</italic> and other stresses. Furthermore, 99 resistance gene analogues (RGA) and 112 transcription factors (TF) were screened out from the above common genes, which were utilized to construct gene co-expression networks (GCEN). Based on the Top 20 of the connection degrees, hub genes were identified in the GCEN. Among them, <italic>OsJAMyb</italic>, <italic>bsr-d1</italic>, and <italic>OsWRKY76</italic> had been reported to be against rice blast, and <italic>OsSPL9</italic> was related to resistance to rice stripe virus. The left hub genes were considered as important potential resistance genes which need further functional verification to prepare for breeding broad-spectrum resistance rice cultivars.

Superior Capsular Reconstruction: A Salvage Option for Massive Irreparable Rotator Cuff Tears with Pseudoparalysis or Subscapularis Insufficiency

We sought to examine superior capsular reconstruction (SCR) outcomes after minimum 2-year follow-up and determine risk factors that were predictive of outcomes. Forty consecutive patients (mean age 57.3 years, 87.5% male) who underwent SCR for massive irreparable rotator cuff tears (RCT) met the inclusion criteria. Minimum 2-year follow-up was obtained for 32 patients (80% follow-up). Patient demographics and preoperative clinical findings were collected. Postoperative data, including complications, patient satisfaction, strength and range-of-motion (ROM), and patient-reported outcomes were collected. The Hamada score was ≤2 in 88% with average acromiohumeral interval distance of 6.8 mm. Preoperatively, 6 patients had external rotation lag (19%) and 6 had pseudoparalysis (19%). Intraoperative assessment of the subscapularis demonstrated true insufficiency in 38%. There was significant improvement in forward elevation (FE) (31° increase; P= .007) and strength in all planes (all P < .05). Patient-reported outcomes significantly improved (American Shoulder and Elbow Surgeon [ASES] 34-point increase; visual analog scale [VAS] 2.9-point decrease; single alpha-numeric evaluation [SANE] 48-point increase; all P < .05). Twenty-six patients (81%) were completely or somewhat satisfied with surgery. At time of final follow-up, 3/32 patients (9%) failed SCR and converted to reverse total shoulder arthroplasty. There were 4 (13%) reported complications (2 patients had postoperative falls; 1 patient had persistent severe pain; 1 had persistent stiffness). One patient was deceased. Patients with pseudoparalysis (n= 6) had significant improvement in post-operative FE (28 vs 154°; P < .0001) and SANE score (P= .016) with 66% patient satisfaction. However, outcome scores overall remained lower than SCR without pseudoparalysis. Regarding subscapularis insufficiency (n= 12), significant improvement was seen in postoperative FE (108 vs 158°; P= .019) and patient-reported outcome scores (P < .005). In patients converted from SCR to reverse total shoulder arthroplasty (n= 3), there were no distinguishing characteristics present. Superior capsular reconstruction is an effective salvage operation for massive irreparable RCT. Patients with pseudoparalysis or subscapularis insufficiency demonstrate significant postoperative improvement in FE and patient-reported outcomes. IV, retrospective cohort.

First high-resolution genetic linkage map of taimen (Hucho taimen) and its application in QTL analysis of growth-related traits

Taimen (Hucho taimen) is an excellent aquaculture species. Currently, no selective breeding program has been conducted. To promote molecular breeding for taimen, we used genotype-by-sequencing technology to construct a high-resolution linkage map and performed QTL studies of growth-related traits. We sequenced 177 individuals of two full-sib families and obtained 58,016 SNPs. Among them, 30,535 SNPs were assigned to 42 linkage groups. The linkage map contained 6734 unique loci and spanned 4253.484 cM in total, with an average interval distance of 0.657 cM. The length for each linkage group ranged from 66.257 cM to 135.533 cM, with an average interval distance of 0.468 cM to 1.110 cM. This SNP linkage map integrated 65.1% scaffolds of the Hucho hucho genome to form 42 pseudo-chromosomes, with a mean correlation coefficiency of 0.893 between the linkage map and the genome. Based on this high-resolution linkage map, we performed QTL analyses of four growth-related traits of taimen aged 6–7 months. The analyses discovered 27 QTLs, including 18 QTLs for body weight, 5 QTLs for standard length, 3 QTLs for body thickness, and 1 QTL for body height. Based on Hucho hucho genome annotation, 487 genes within QTL regions were enriched in metabolism-related pathways; these genes could serve as candidate genes associated with the growth of taimen. The linkage map and QTLs obtained in this study provide useful tools for genetic studies and molecular breeding of taimen.

High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill.

The Chinese jujube (Ziziphus jujuba Mill., 2n = 2x = 24), one of the most popular fruit trees in Asia, is widely cultivated and utilized in China, where it is traditionally consumed as both a fresh and dried food resource. A high-density genetic map can provide the necessary framework for quantitative trait loci (QTL) analyses and map-based gene cloning and molecular breeding. In this study, we constructed a new high-density genetic linkage map via a genotyping-by-sequencing approach. For the consensus linkage map, a total of 3,792 markers spanning 2,167.5 cM were mapped onto 12 linkage groups, with an average marker interval distance of 0.358 cM. The genetic map anchored 301 Mb (85.7%) of scaffolds from the sequenced Z. jujuba “Junzao” genome. Based on this genetic map, 30 potential QTLs were detected, including 27 QTLs for leaf traits and 3 QTLs for needling length. This high-density genetic map and the identified QTLs for relevant agronomic traits lay the groundwork for functional genetic mapping, map-based cloning, and marker-assisted selection in jujube.

Construction of a genetic linkage map of Lentinula edodes based on SSR, SRAP and TRAP markers.

Genetic mapping is a basic tool for eukaryotic genomic research. It allows the localization of genes or quantitative trait loci (QTLs) and map-based cloning. In this study, we constructed a linkage map based on DNA samples from a commercial strain L808, including two parental monokaryons and 93 single spore isolates considered with segregating to 1:1:1:1 at four mating types (A1B1, A1B2, A2B1 and A2B2). Using Simple Sequence Repeats (SSR), Sequence Related Amplified Polymorphism (SRAP), Target Region Amplified Polymorphism (TRAP) molecular markers, 182 molecular markers and two mating factors were located on 11 linkage groups (LGs). The total length of the map was 948.083 centimorgan (cM), with an average marker interval distance of 4.817 cM. Only two gaps spanning more than 20 cM was observed. The probability of 20 cM, 10 cM, 5 cM genetic distance cover one marker was 99.68%, 94.36%, 76.43% in our genetic linkage map, respectively. This is the first linkage map of Lentinula edodes using SSR markers, which provides essential information for quantitative trait analyses and improvement of genome assembly.

Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology

BackgroundRestriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe.ResultsWe established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation.ConclusionsThe set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.

De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies.

BackgroundRestriction site associated DNA sequencing (RAD-seq), a next-generation sequencing technology, has greatly facilitated genetic linkage mapping studies in outbred species. RAD-seq is capable of discovering thousands of genetic markers for linkage mapping across many individuals, and can be applied in species with or without a reference genome. Although several analytical tools are available for RAD-seq data, alternative strategies are necessary for improving the marker quality and hence the genetic mapping accuracy.ResultsWe demonstrate a strategy for constructing dense genetic linkage maps in hybrid forest trees by combining RAD-seq and whole-genome sequencing technologies. We performed RAD-seq of 150 progeny and whole-genome sequencing of the two parents in an F1 hybrid population of Populus deltoides × P. simonii. Two rough references were assembled from the whole-genome sequencing reads of the two parents separately. Based on the parental reference sequences, 3442 high-quality single nucleotide polymorphisms (SNPs) were identified that segregate in the ratio of 1:1. The maternal linkage map of P. deltoides was constructed with 2012 SNPs, containing 19 linkage groups and spanning 4067.16 cM of the genome with an average distance of 2.04 cM between adjacent markers, while the male map of P. simonii consisted of 1430 SNPs and the same number of linkage groups with a total length of 4356.04 cM and an average interval distance of 3.09 cM. Collinearity between the parental linkage maps and the reference genome of P. trichocarpa was also investigated. Compared with the result on the basis of the existing reference genome, our strategy identified more high-quality SNPs and generated parental linkage groups that nicely match the karyotype of Populus.ConclusionsThe strategy of simultaneously using RAD and whole-genome sequencing technologies can be applied to constructing high-density genetic maps in forest trees regardless of whether a reference genome exists. The two parental linkage maps constructed here provide more accurate genetic resources for unraveling quantitative trait loci and accelerating molecular breeding programs, as well as for comparative genomics in Populus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3003-9) contains supplementary material, which is available to authorized users.

Enrichment of Genetic Linkage Maps and Mapping QTLs Specific to Seed Strength-Hardness/Softness-In Guava (Psidium guajava L.)

The present research focuses mainly on molecular mining and morphological evaluation of guava genome within a full-sib population and, thereby, mapping of quantitative trait loci related to fruit quality traits, viz., seed strength (hardness/softness) and average fruit weight. Linkage maps were enriched for both parental lines, 'Kamsari' and 'Purple Local' using a set of 60 RAPD markers following the pseudo-testcross strategy on a panel of 94 progeny. A total of 480 scorable markers were identified, of which 131 were specific to 'kamsari' and 28 to 'Purple Local', segregating as test cross markers, and, 321 showing intercross pattern common to both. 'Kamsari' spanned a total length of 1959.1cM with average marker interval distance of 3.93cM, while 'Purple Local' spanned a length of 1537.9cM with average marker interval distance of 3.29cM, by forming 11 linkage groups. Estimated genome length observed was 93.02% and 92.77% in 'Kamsari' and 'Purple Local', respectively. Composite Interval Mapping (CIM) was computed at significance of 0.05 and LOD threshold greater than 3.0, which led to detection of one major QTL for the trait of average fruit weight, and, four QTLs for the trait of seed strength (hardness/softness). Of these, two were major and two minor QTLs. Our study provides molecular mapping information on marker-assisted selection for improvement of guava in a breeding program.

Construction of High-Density Linkage Maps of Populus deltoides × P. simonii Using Restriction-Site Associated DNA Sequencing.

Although numerous linkage maps have been constructed in the genus Populus, they are typically sparse and thus have limited applications due to low throughput of traditional molecular markers. Restriction-site associated DNA sequencing (RADSeq) technology allows us to identify a large number of single nucleotide polymorphisms (SNP) across genomes of many individuals in a fast and cost-effective way, and makes it possible to construct high-density genetic linkage maps. We performed RADSeq for 299 progeny and their two parents in an F1 hybrid population generated by crossing the female Populus deltoides ‘I-69’ and male Populus simonii ‘L3’. A total of 2,545 high quality SNP markers were obtained and two parent-specific linkage maps were constructed. The female genetic map contained 1601 SNPs and 20 linkage groups, spanning 4,249.12 cM of the genome with an average distance of 2.69 cM between adjacent markers, while the male map consisted of 940 SNPs and also 20 linkage groups with a total length of 3,816.24 cM and an average marker interval distance of 4.15 cM. Finally, our analysis revealed that synteny and collinearity are highly conserved between the parental linkage maps and the reference genome of P. trichocarpa. We demonstrated that RAD sequencing is a powerful technique capable of rapidly generating a large number of SNPs for constructing genetic maps in outbred forest trees. The high-quality linkage maps constructed here provided reliable genetic resources to facilitate locating quantitative trait loci (QTLs) that control growth and wood quality traits in the hybrid population.

A genetic linkage map with 178 SSR and 1 901 SNP markers constructed using a RIL population in wheat (Triticum aestivum L.)

The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat (Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1, 703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

Development of SRAP and SSR marker-based genetic linkage maps of guava (Psidium guajava L.)

In the present study genotyping of guava full-sib population with 94 F1 progenies, derived from a two-way pseudo-testcross strategy differing in fruit quality traits such as seed strength (hardness/softness), fruit weight, and TSS, was carried out using simple sequence repeat (SSR) markers and sequence-related amplified polymorphic (SRAP) primer combinations. In the case of SSR's high-throughput genotyping, through a M13-Tailed PCR principle, using a set of 160 SSR primer pairs revealed 64.3% parental polymorphism that generated 321 alleles during the mapping population survey. Twenty percent of parental polymorphism was revealed with SRAPs that generated 126 scorable markers. Two linkage maps were constructed for parents using maternal-specific 143 testcross marker loci and paternal-specific 127 testcross markers along with 60 intercross marker loci. At a minimum logarithm of the odds (LOD) score of 4.0 and a maximum map distance of 40cM the maternal Kamsari map covered 2551.3cM with an average marker interval distance of 13.21cM having a total of 193 framework marker loci being ordered into 11 linkage groups. The paternal Purple Local map covered 2113.0cM with an average marker interval distance of 12.07cM having 175 framework marker loci being ordered into 11 linkage groups. The estimated genome coverage was of 87.32% in Kamsari and 83.74% in Purple Local. These genetic maps will play a pivotal role in identification of complex quantitative trait loci (QTLs) related to fruit quality. This is the first report of linkage maps in guava based on the combination of SSR along with SRAP markers.

Meso-scale wrinkled coatings to improve heat transfers of surfaces facing ambient air

Meso-scale (micrometer-to submillimeter-scale) wrinkled surfaces coated on steel sheets used in outdoor storage and transport facilities for industrial low-temperature liquids were discovered to efficiently increase convective heat transfer between ambient air and the surface. The radiative and convective heat transfer coefficients of various wrinkled surfaces, which were formed by coating steel sheets with several types of shrinkable paints, were examined. The convective heat transfer coefficient of a surface colder than ambient air monotonically changed with average height difference and interval distance of the wrinkle undulation, where the proportions were 0.0254 and 0.0054 W/m2/K/μm, respectively. With this wrinkled coating, users can lower the possibility of condensation and reduce rust and maintenance cost of facilities for industrial low-temperature liquids. From the point of view of manufacturers, this coating method can be easily adapted to conventional manufacturing processes.

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

Brown rot (BR) caused by Monilinia spp. leads to significant post-harvest losses in stone fruit production, especially peach. Previous genetic analyses in peach progenies suggested that BR resistance segregates as a quantitative trait. In order to uncover genomic regions associated with this trait and identify molecular markers for assisted selection (MAS) in peach, an F1 progeny from the cross “Contender” (C, resistant) × “Elegant Lady” (EL, susceptible) was chosen for quantitative trait loci (QTL) analysis. Over two phenotyping seasons, skin (SK) and flesh (FL) artificial infections were performed on fruits using a Monilinia fructigena isolate. For each treatment, infection frequency (if) and average rot diameter (rd) were scored. Significant seasonal and intertrait correlations were found. Maturity date (MD) was significantly correlated with disease impact. Sixty-three simple sequence repeats (SSRs) plus 26 single-nucleotide polymorphism (SNP) markers were used to genotype the C × EL population and to construct a linkage map. C × EL map included the eight Prunus linkage groups (LG), spanning 572.92 cM, with an average interval distance of 6.9 cM, covering 78.73 % of the peach genome (V1.0). Multiple QTL mapping analysis including MD trait as covariate uncovered three genomic regions associated with BR resistance in the two phenotyping seasons: one containing QTLs for SK resistance traits near M1a (LG C × EL-2, R 2 = 13.1–31.5 %) and EPPISF032 (LG C × EL-4, R 2 = 11–14 %) and the others containing QTLs for FL resistance, near markers SNP_IGA_320761 and SNP_IGA_321601 (LG3, R 2 = 3.0–11.0 %). These results suggest that in the C × EL F1 progeny, skin resistance to fungal penetration and flesh resistance to rot spread are distinguishable mechanisms constituting BR resistance trait, associated with different genomic regions. Discovered QTLs and their associated markers could assist selection of new cultivars with enhanced resistance to Monilinia spp. in fruit.

An EST-based linkage map reveals chromosomal translocation in Capsicum

To facilitate marker-assisted breeding and analysis of the structure and/or organization of Capsicum (pepper) genomes, this study utilized expressed sequence tags (ESTs) to develop single-nucleotide polymorphism (SNP) markers. Three different types of PCR-based markers derived from pepper ESTs were developed: intron-based polymorphic markers (IBPs), conserved ortholog sets (COSIIs), and eSNPs (EST–SNPs). For scanning and detection of SNPs, high-resolution melting analysis was performed and the resultant markers were used for linkage analysis. A total of 512 markers, comprising 214 IBP, 143 COSII, 48 eSNP, and 107 previously reported markers, were mapped on 12 linkage groups (LGs) of the “AC99” F2 population. This newly constructed interspecific map (AC2) covered 2,335.6 cM with an average marker interval distance of 4.5 cM and was aligned directly with another interspecific map (AF) for validation. Most LGs showed collinear relationships, except for the alignment of chromosomes 1 and 8 of the AC2 map to LG P1 of the AF map. Using our newly developed SNP markers, we generated chromosome-specific markers, and the previously predicted reciprocal translocation event between chromosomes 1 and 8 was revealed between wild and cultivated Capsicum by fluorescent in situ hybridization analysis. The results from this study will promote subsequent evolutionary studies of Capsicum species.

SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance

Ascochyta blight, caused by the fungus Ascochyta fabae Speg., is a common and destructive disease of faba bean (Vicia faba L.) on a global basis. Yield losses vary from typical values of 35–40% to 90% under specific environmental conditions. Several sources of resistance have been identified and used in breeding programs. However, introgression of the resistance gene determinants into commercial cultivars as a gene pyramiding approach is reliant on selection of closely linked genetic markers. A total of 14,552 base variants were identified from a faba bean expressed sequence tag (EST) database, and were further quality assessed to obtain a set of 822 high-quality single nucleotide polymorphisms (SNPs). Sub-sets of 336 EST-derived simple sequence repeats (SSRs) and 768 SNPs were further used for high-density genetic mapping of a biparental faba bean mapping population (Icarus×Ascot) that segregates for resistance to ascochyta blight. The linkage map spanned a total length of 1216.8cM with 12 linkage groups (LGs) and an average marker interval distance of 2.3cM. Comparison of map structure to the genomes of closely related legume species revealed a high degree of conserved macrosynteny, as well as some rearrangements. Based on glasshouse evaluation of ascochyta blight resistance performed over two years, four genomic regions controlling resistance were identified on Chr-II, Chr-VI and two regions on Chr-I.A. Of these, one (QTL-3) may be identical with quantitative trait loci (QTLs) identified in prior studies, while the others (QTL-1, QTL-2 and QTL-4) may be novel. Markers in close linkage to ascochyta blight resistance genes identified in this study can be further validated and effectively implemented in faba bean breeding programs.

Construction of Genetic Map and Analysis of QTLs for Grain Weight Using a RIL Population Derived from Shannong 01-35 × Gaocheng 9411

The objectives of this study were to construct a new linkage map of wheat using a recombinant inbred line (RIL) population derived from the cross between Shannong 01-35 and Gaocheng 9411 and locate quantitative trait loci for thousand-grain weight (TGW) using this map. The RIL population, consisting of 182 lines, was obtained via single-seed descendent method until the F 8 generation. The genetic map consisted of one TaGW2-CAPS,59 SSR, and442 DArT markers in 29 linkage groups, including 54 novel markers (44 DArT markers and 10 SSRs) assigned into 18 linkage groups. The total genetic length of the map was 4084.5 cM with an average interval distance of 8.13 cM. The 182 RILs and their parents were grown in four environments from 2008 to 2010, and QTLs associated with TGW were identified using mixed linear model based on both separated and joint environments. A total of seven QTLs were detected including three QTLs ( QGW4B-7 , QGW5B-20 , and QGW6A-29 ) commonly found using both methods. Three major QTLs, i.e., QGW4B-7 , QGW5B-12 , and QGW6A-29 , exhibited phenotypic contributions higher than 10%. These results suggest that the QTLs detected by using the successfully constructed genetic map are valuable in molecular marker-assisted selection in wheat.

Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene

Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (S(sh)) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6S(sh)) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.