Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones

Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.     

Identification of the quantitative trait loci (QTL) underlying water soluble protein content in soybean

Water soluble protein content (SPC) plays an important role in the functional efficacy of protein in food products. Therefore, for the identification of quantitative trait loci (QTL) associated with SPC, 212 F_2:9 lines of the recombinant inbred line (RIL) population derived from the cross of ZDD09454 × Yudou12 were grown along with the parents, in six different environments (location × year) to determine inheritance and map solubility-related genes. A linkage map comprising of 301 SSR markers covering 3,576.81 cM was constructed in the RIL population. Seed SPC was quantified with a macro-Kjeldahl procedure in samples collected over multiple years from three locations (Nantong in 2007 and 2008, Zhengzhou in 2007 and 2008, and Xinxiang in 2008 and 2009). SPC demonstrated transgressive segregation, indicating a complementary genetic structure between the parents. Eleven putative QTL were associated with SPC explaining 4.5–18.2 % of the observed phenotypic variation across the 6 year/location environments. Among these, two QTL (qsp8-4, qsp8-5) near GMENOD2B and Sat_215 showed an association with SPC in multiple environments, suggesting that they were key QTL related to protein solubility. The QTL × environment interaction demonstrated the complex genetic mechanism of SPC. These SPC-associated QTL and linked markers in soybean will provide important information that can be utilized by breeders to improve the functional quality of soybean varieties.     

Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman)

Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex × Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0–9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% < R ² < 27%). The loci were within the intervals Satt632–A2D8 on linkage group (LG) A2 (chromosome 8); Satt583–Satt415 on LG B1 (11); Satt009–Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R ² < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R ² < 24%) between Satt632–A2D8 on LG A2 (8) and Sat_039–Satt160 on LG F (13); and a major locus effect (R ² = 54%) for antibiosis on LG D2 (17) between Satt464–Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying resistance to nematode or insect pests (LGs G, H and M).     

Linkage analysis and identification of quantitative trait loci associated with freeze tolerance and turf quality traits in St. Augustinegrass

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass commonly grown in the southern USA. In this study, the first linkage map for all nine haploid chromosomes of the species was constructed for cultivar ‘Raleigh’ and cultivar ‘Seville’ using a pseudo-F₂ mapping strategy. A total of 160 simple sequence repeat markers were mapped to nine linkage groups (LGs) covering a total distance of 1176.24 cM. To demonstrate the usefulness of the map, quantitative trait loci (QTL) were mapped controlling field winter survival, laboratory-based freeze tolerance, and turf quality traits. Multiple genomic regions associated with these traits were identified. Moreover, overlapping QTL were found for winterkill and spring green up on LG 3 (99.21 cM); turf quality, turf density, and leaf texture on LG 3 (68.57–69.50 cM); and surviving green tissue and regrowth on LGs 1 (38.31 cM), 3 (77.70 cM), 6 (49.51 cM), and 9 (34.20 cM). Additional regions, where QTL identified in both field and laboratory-based/controlled environment freeze testing co-located, provided strong support that these regions are good candidates for true gene locations. These results present the first complete linkage map produced for St. Augustinegrass, providing a template for further genetic mapping. Additionally, markers linked to the QTL identified may be useful to breeders for transferring these traits into new breeding lines and cultivars.     

Comparative mapping of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait

Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F₂ mapping population derived by crossing the inbred lines ‘835’ (susceptible) and ‘B2’ (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1,041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-year experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them.     

Analysis of an intraspecific RIL population uncovers genomic segments harbouring multiple QTL for seed relevant traits in lentil (<Emphasis Type="Italic">Lens culinaris</Emphasis> L.)

Improving seed related traits remains key objective in lentil breeding. In recent years, genomic resources have shown great promise to accelerate crop improvement. However, limited genomic resources in lentil greatly restrict the use of genomics assisted breeding. The present investigation aims to build an intraspecific genetic linkage map and identify the QTL associated with important seed relevant traits using 94 recombinant inbreds (WA 8649090 × Precoz). A total of 288 polymorphic DNA markers including simple sequence repeat (SSR), inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) were assayed on mapping population. The resultant genetic linkage map comprised 220 loci spanning 604.2 cM of the lentil genome, with average inter-marker distance of 2.74 cM. QTL mapping in this RIL population uncovered a total of 18 QTL encompassing nine major and nine minor QTL. All major QTL were detected for seed related traits viz., seed diameter (SD), seed thickness (ST), seed weight (SW) and seed plumpness (SP) across two locations. A considerable proportion of the phenotypic variation (PV) was accounted to these QTL. For instance, one major QTL on LG5 controlling SW (QTL 15) explained 50% PV in one location, while the same QTL accounted for 34.18% PV in other location. Importantly, the genomic region containing multiple QTL for different seed traits was mapped to a 17-cM region on LG5. The genomic region harbouring QTL for multiple traits opens up exciting opportunities for genomics assisted improvement of lentil.     

Identification of germplasm with stacked QTL underlying seed traits in an inbred soybean population from cultivars Essex and Forrest

Soybean (Glycine max (L.) Merr.) seed provides valuable oil (~200 g/kg) and protein (~400 g/kg) co-products. Seed composition variations result from several quantitative trait loci (QTL) that act through development. The objectives here were to identify loci underlying seed traits in the Essex × Forrest (EF94)-derived recombinant inbred line (RIL) population which has low frequencies of marker polymorphisms. Seed weight, protein, and oil were measured over 3 years: 2001, 2003, and 2005. Essex’s seeds were larger (141 mg/seed), higher in protein (406 g/kg), and lower in oil (190 g/kg) than Forrest’s (115 mg/seed, 395 g protein/kg, and 203 g oil/kg). Marker analysis included 413 markers for trait associations used for ANOVA, interval mapping, and composite interval mapping. Eleven QTL in nine genomic regions were associated (LOD >2; P < 0.0077) with seed traits. Two QTL, for mean protein and seed size, were clustered on linkage group (LG) E (chromosome Gm16). QTL for protein content alone were found on LG C2 (Gm6), LG D1b (Gm2), LG H (Gm12), and LG I (Gm20). The alleles from Essex, the high-protein parent, underlay higher protein (4–10 g/kg) at four of five loci. A QTL for mean oil was found on LG A2 (Gm18) and on LG I (Gm 20). The alleles from Forrest underlay higher oil (3–4 g/kg). Five separate QTL for mean seed weight were found on LG A1 (Gm05), LG N (Gm15), two on LG B1 (Gm11) and one on LG N (Gm3). The alleles from Essex underlay greater seed weight (0.4–0.66 g/100 seeds). The QTL positions were consistent with reported loci. Germplasm that contained all five beneficial alleles at the QTL underlying protein was significantly higher in protein and yield than Essex (409.7–412.3 g/kg) and included RILs 49 and 62. The germplasm identified can be useful for further breeding of the many traits and QTL measured in each line.     

Qualitative and quantitative trait loci conditioning resistance to Puccinia coronata pathotypes NQMG and LGCG in the oat (Avena sativa L.) cultivars Ogle and TAM O-301

Mapping disease resistance loci relies on the type and precision of phenotypic measurements. For crown rust of oat, disease severity is commonly assessed based on visual ratings of infection types (IT) and/or diseased leaf area (DLA) of infected plants in the greenhouse or field. These data can be affected by several variables including; (i) non-uniform disease development in the field; (ii) atypical symptom development in the greenhouse; (iii) the presence of multiple pathogenic races or pathotypes in the field, and (iv) rating bias. To overcome these limitations, we mapped crown rust resistance to single isolates in the Ogle/TAM O-301 (OT) recombinant inbred line (RIL) population using detailed measurements of IT, uredinia length (UL) and relative fungal DNA (FDNA) estimates determined by q-PCR. Measurements were taken on OT parents and recombinant inbred lines (RIL) inoculated with Puccinia coronata pathotypes NQMG and LGCG in separate greenhouse and field tests. Qualitative mapping identified an allele conferred by TAM O-301 on linkage group (LG) OT-11, which produced a bleached fleck phenotype to both NQMG and LGCG. Quantitative mapping identified two major quantitative trait loci (QTL) originating from TAM O-301 on LGs OT-11 and OT-32 which reduced UL and FDNA of both isolates in all experiments. Additionally, minor QTLs that reduced UL and FDNA were detected on LGs OT-15 and OT-8, originating from TAM O-301, and on LG OT-27, originating from Ogle. Detailed assessments of the OT population using two pathotypes in both the greenhouse and field provided comprehensive information to effectively map the genes responsible for crown rust resistance in Ogle and TAM O-301 to NQMG and LGCG.     

Quantitative trait locus mapping reveals conservation of major and minor loci for powdery mildew resistance in four sources of resistance in mungbean [Vigna radiata (L.) Wilczek]

Powdery mildew (PM) is a common and serious disease of mungbean [Vigna radiata (L.) Wilczek]. A few quantitative trait loci (QTL) for PM resistance in mungbean have been reported. The objective of this study was to locate QTL for PM resistance in two resistant accessions V4718 and RUM5. Simple sequence repeat markers were analyzed in an F₂ population from a cross between Kamphaeng Saen 1 (KPS1; susceptible to PM) and V4718 (resistant to PM), and in F₂ and BC₁F₁ populations from a cross between Chai Nat 60 (CN60; susceptible to PM) and RUM5 (resistant to PM). Progenies of 134 F_2:3 and F_2:4 lines derived from KPS1 × V4718, and 190 F_2:3 and 74 BC₁F_1:2 lines derived from CN60 × RUM5 and CN60 × (CN60 × RUM5), respectively, were evaluated for response to PM under field conditions. Multiple interval mapping identified a major QTL on linkage group (LG) 9 and two minor QTL on LG4 for the resistance in V4718, and detected two major QTL on LG6 and LG9 and one minor QTL on LG4 for the resistance in RUM5. Comparative linkage analysis of the QTL for PM resistance in this study and in previous reports suggests that the resistance QTL on LG9 in V4718, RUM5, ATF3640 and VC6468-11-1A are the same locus or linked. One QTL on LG4 is the same in three sources (V4718, RUM5 and VC1210A). Another QTL on LG6 is the same in two sources (RUM5 and VC6468-11-1A). In addition, one QTL in V4718 on LG4 appears to be a new resistance locus. These different resistance loci will be useful for breeding durably PM-resistant mungbean cultivars.     

Multi-environment QTL analyses for drought-related traits in a recombinant inbred population of chickpea (Cicer arientinum L.)

A recombinant inbred line (RIL) population, comprising 181 lines derived from ILC588 × ILC3279, was evaluated in 10 environments across three locations with different moisture gradients. A drought resistance score (DRS) and three phenology traits—plant height (PLHT), days to flowering (DFLR), and days to maturity (MAT)—were recorded along with seven yield-related traits—grain yield (GY), biological yield (BY), harvest index (HI), the number of pods/3 plants (Pod), percentage of empty pods (%Epod), 100 seed weight (100 sw), and seed number/3 plants (SN). Two RILs (152, 162) showed the best GYs and DRSs under stressed and non-stressed environments. The quantitative trait loci (QTLs) analyses detected 93 significant QTLs (LOD ≥ 2.0) across the genome × environment interactions. The highest phenotypic variation (>24 %) was explained by the QTL_DFLR in Terbol-11. Four common possible pleiotropic QTLs on LG3 and LG4 were identified as associated with DFLR, DRS, GY, MAT, HI, SN, and Pod. No significant epistatic interactions were found between these QTLs and the other markers. However, the QTL for DRS was detected as a conserved QTL in three late planting environments. The markers H6C-07 (on LG3) and H5G01 (on LG4) were associated with QTLs for many traits in all environments studied except two. The allele ‘A’ of marker H6C07 (from the tolerant parent ILC588) explained 80 % of the yield increase under late planting and 29.8 % of that under dry environments. Concentrating on LG3 and LG4 in molecular breeding programs for drought could speed up improvement for these traits.     

Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection

Association mapping based on the linkage disequilibrium provides a promising tool to identify genes responsible for quantitative variations underlying complex traits. Presented here is a maize association mapping panel consisting of 155 inbred lines with mainly temperate germplasm, which was phenotyped for 34 traits and genotyped using 82 SSRs and 1,536 SNPs. Abundant phenotypic and genetic diversities were observed within the panel based on the phenotypic and genotypic analysis. A model-based analysis using 82 SSRs assigned all inbred lines to two groups with eight subgroups. The relative kinship matrix was calculated using 884 SNPs with minor allele frequency ≥20% indicating that no or weak relationships were identified for most individual pairs. Three traits (total tocopherol content in maize kernel, plant height and kernel length) and 1,414 SNPs with missing data <20% were used to evaluate the performance of four models for association mapping analysis. For all traits, the model controlling relative kinship (K) performed better than the model controlling population structure (Q), and similarly to the model controlling both population structure and relative kinship (Q + K) in this panel. Our results suggest this maize panel can be used for association mapping analysis targeting multiple agronomic and quality traits with optimal association model.     

Genetic variation at bx1 controls DIMBOA content in maize

The main hydroxamic acid in maize (Zea mays L.) is 2-4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA). DIMBOA confers resistance to leaf-feeding by several corn borers. Most genes involved in the DIMBOA metabolic pathway are located on the short arm of chromosome 4, and quantitative trait loci (QTLs) involved in maize resistance to leaf-feeding by corn borers have been localized to that region. However, the low resolution of QTL linkage mapping does not allow convincing proof that genetic variation at bx loci was responsible for the variability for resistance. This study addressed the following objectives: to determine the QTLs involved in DIMBOA synthesis across genetically divergent maize inbreds using eight RIL families from the nested association mapping population, to check the stability of QTLs for DIMBOA content across years by evaluating two of those RIL families in 2 years, and to test the involvement of bx1 by performing association mapping with a panel of 281 diverse inbred lines. QTLs were stable across different environments. A genetic model including eight markers explained approximately 34% of phenotypic variability across eight RIL families and the position of the largest QTL co-localizes with the majority of structural genes of the DIMBOA pathway. Candidate association analysis determined that sequence polymorphisms at bx1 greatly affects variation of DIMBOA content in a diverse panel of maize inbreds, but the specific causal polymorphism or polymorphisms responsible for the QTL detected in the region 4.01 were not identified. This result may be because the causal polymorphism(s) were not sequenced, identity is masked by linkage disequilibrium, adjustments for population structure reduce significance of causal polymorphisms or multiple causal polymorphisms affecting bx1 segregate among inbred lines.     

Identification and validation of a major cadmium accumulation locus and closely associated SNP markers in North Dakota durum wheat cultivars

Durum wheat has the tendency of accumulating more cadmium (Cd), a biotoxic heavy metal, in seeds than other commonly grown cereals, thus posing a serious food safety/public health concern. This could have serious negative impact on the national pasta industry and the international export market of durum wheat. The phenotyping for selecting low Cd lines is expensive and time consuming. The use of markers could be a more sustainable approach for selecting lines with low Cd levels. Here, a RIL population developed from a cross between Grenora (high Cd) × Haurani (low Cd) and two association mapping panels consisting of advanced breeding lines from the North Dakota durum wheat breeding program were used to identify QTL and associated markers for Cd. A major QTL, with Haurani contributing low Cd uptake allele and explaining 54.3 % phenotypic variation, was detected on chromosome 5BL. Association mapping using 2010 collection validated the results of linkage mapping and identified major QTL on 5BL. The 2009 collection, showed the presence of a major QTL on chromosome 2B. The SNP marker associated with major QTL on 5BL was converted to user friendly KASPar assay. The major QTL and associated KASPar marker were further validated using another RIL population developed from a cross of Strongfield (low Cd) and Alkabo (high Cd). The development of suitable marker assay, associated with major Cd uptake QTL, would help the selection for low Cd accumulating lines, minimizing the costly phenotypic evaluation for this important trait.     

A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.)

We report the first complete microsatellite genetic map of jute (Corchorus olitorius L.; 2n = 2 × = 14) using an F₆ recombinant inbred population. Of the 403 microsatellite markers screened, 82 were mapped on the seven linkage groups (LGs) that covered a total genetic distance of 799.9 cM, with an average marker interval of 10.7 cM. LG5 had the longest and LG7 the shortest genetic lengths, whereas LG1 had the maximum and LG7 the minimum number of markers. Segregation distortion of microsatellite loci was high (61%), with the majority of them (76%) skewed towards the female parent. Genomewide non-parametric single-marker analysis in combination with multiple quantitative trait loci (QTL)-models (MQM) mapping detected 26 definitive QTLs for bast fibre quality, yield and yield-related traits. These were unevenly distributed on six LGs, as co-localized clusters, at genomic sectors marked by 15 microsatellite loci. LG1 was the QTL-richest map sector, with the densest co-localized clusters of QTLs governing fibre yield, yield-related traits and tensile strength. Expectedly, favorable QTLs were derived from the desirable parents, except for nearly all of those for fibre fineness, which might be due to the creation of new gene combinations. Our results will be a good starting point for further genome analyses in jute.     

Inheritance of reproductive phenology traits and related QTL identification in apricot

Reproductive phenological traits of great agronomical interest in apricot species, including flowering date, ripening date and fruit development period, were studied during 3 years in two F₁ progenies derived from the crosses ‘Bergeron’ × ‘Currot’ (B × C) and ‘Goldrich’ × ‘Currot’ (G × C). Results showed great variability and segregation in each population, confirming the polygenic nature and quantitative inheritance of all the studied traits. Genetic linkage maps were constructed combining SSR and SNP markers, using 87 markers in the ‘B × C’ population and 89 markers in ‘G × C’. The genetic linkage maps in both progenies show the eight linkage groups (LGs) of apricot, covering a distance of 394.9 cM in ‘Bergeron’ and of 414.3 cM in ‘Currot’. The ‘Goldrich’ and ‘Currot’ maps were of 353.5 and 422.3 cM, respectively. The average distance obtained between markers was thus 7.59 cM in ‘Bergeron’ and 7.53 cM in ‘Currot’, whereas the ‘Goldrich’ and ‘Currot’ averages were 5.6 and 7.5 cM, respectively. According to the polygenic nature of the studied phenology traits, QTLs linked to flowering date, ripening date and the fruit development period were identified during the 3 years of the study in all LGs except for LG 8. Among the QTLs identified, major QTLs for flowering and ripening date and the fruit development period were identified in LG 4, especially important in the ‘G × C’ population.     

Mapping QTLs for morpho-agronomic traits in proso millet (<Emphasis Type="Italic">Panicum miliaceum</Emphasis> L.)

Proso millet (Panicum miliaceum L.) is the cereal crop with the low water requirement and increasingly being used for human consumption. It is the most common rotational crop within wheat-based dryland production systems in the semiarid High Plains of the USA. However, there is no published genetic map for this species, which prevents the identification of quantitative trait loci (QTL). The objectives of the present study were (1) construction of a genetic linkage map and (2) identification of DNA markers linked to QTLs for morpho-agronomic traits. A total of 93 recombinant inbred lines derived from a single F₁ (“Huntsman” × “Minsum”) were genotyped with GBS-SNP markers and phenotyped for nine morpho-agronomic traits in the field during 2013 and 2014 at Scottsbluff and Sidney, NE. IciMapping v.4.0.6.0 was used for constructing a genetic linkage map and mapping QTL. The RILs exhibited significant variation for a wide range of traits, and several traits showed evidence of genotype × environment interactions. A total of 833 GBS-SNP markers formed 18 major and 84 minor linkage groups, whereas 519 markers remained ungrouped. A total of 117 GBS-SNP markers were distributed on the 18 major linkage groups spanning a genome length of 2137 cM of proso millet with an average distance of 18 cM between markers. The length and number of markers in each of the 18 major linkage groups ranged from 54.6 to 236 cM and 4 to 12, respectively. A total of 18 QTLs for eight morpho-agronomic traits were detected on 14 linkage groups, each of which explained 13.2–34.7 % phenotypic variance. DNA markers flanking the QTLs were identified, which will aid in marker-assisted selection of these traits. To our knowledge, this is the first genetic linkage map and QTL mapping in proso millet, which will support further genetic analysis and genomics-assisted genetic improvement of this crop.     

Introgression of homeologous quantitative trait loci (QTLs) for resistance to the root-knot nematode [Meloidogyne arenaria (Neal) Chitwood] in an advanced backcross-QTL population of peanut (Arachis hypogaea L.)

Resistance to root-knot nematodes [Meloidogyne arenaria (Neal) Chitwood] is needed for cultivation of peanut in major peanut-growing areas, but significant resistance is lacking in the cultivated species (Arachis hypogaea L.). Markers to two closely-linked genes introgressed from wild relatives of peanut have been identified previously, but phenotypic evidence for the presence of additional genes in wild species and introgression lines has eluded quantitative trait locus (QTL) identification. Here, to improve sensitivity to small-effect QTLs, an advanced backcross population from a cross between a Florunner component line and the synthetic amphidiploid TxAG-6 [Arachis batizocoi × (A. cardenasii × A. diogoi)]^4× was screened for response to root-knot nematode infection. Composite interval mapping results suggested a total of seven QTLs plus three putative QTLs. These included the known major resistance gene plus a second QTL on LG1, and a potentially homeologous B-genome QTL on LG11. Additional potential homeologs were identified on linkage group (LG) 8 and LG18, plus a QTL on LG9.2 and putative QTLs on LG9.1 and 19. A QTL on LG15 had no inferred resistance-associated homeolog. Contrary to expectation, two introgressed QTLs were associated with susceptibility, and QTLs at some homeologous loci were found to confer opposite phenotypic responses. Long-term functional conservation accompanied by rapid generation of functionally divergent alleles may be a singular feature of NBS-LRR resistance gene clusters, contributing to the richness of resistance alleles available in wild relatives of crops. The significance for peanut evolution and breeding is discussed.     

A linkage map of chickpea (Cicer arietinum L.) based on populations from Kabuli × Desi crosses: location of genes for resistance to fusarium wilt race 0

Two recombinant inbred line (RIL) populations derived from intraspecific crosses with a common parental line (JG62) were employed to develop a chickpea genetic map. Molecular markers, flower colour, double podding, seed coat thickness and resistance to fusarium wilt race 0 (FOC-0) were included in the study. Joint segregation analysis involved a total of 160 markers and 159 RILs. Ten linkage groups (LGs) were obtained that included morphological markers and 134 molecular markers (3 ISSRs, 13 STMSs and 118 RAPDs). Flower colour (B/b) and seed coat thickness (Tt/tt) appeared to be linked to STMS (GAA47). The single-/double-podding locus was located on LG9 jointly with two RAPD markers and STMS TA80. LG3 included a gene for resistance to FOC-0 (Foc0₁/foc0₁) flanked by RAPD marker OPJ20₆₀₀ and STMS marker TR59. The association of this LG with FOC-0 resistance was confirmed by QTL analysis in the CA2139 × JG62 RIL population where two genes were involved in the resistance reaction. The STMS markers enabled comparison of LGs with preceding maps.     

Identification and validation of quantitative trait loci controlling seed isoflavone content across multiple environments and backgrounds in soybean

Soybean is important throughout the world not only due to the high seed protein and oil but also owing to the seed isoflavone. To improve the isoflavone concentration in seeds, detecting and mining the stable and reliable quantitative trait loci (QTLs) and related genes in multiple environments and genetic backgrounds become more and more important. In view of this, a F_6:7 recombinant inbred line (RIL) population of 345 lines derived from a cross between Zheng 92116 and Liaodou14 (ZL) was genotyped using 1739 polymorphic SNP and 127 SSR markers in this study and was phenotyped for individual and total seed isoflavone in four environments over 2 years. In total, 48 additive QTLs, which explained 3.00–29.83% of seed isoflavone variation, were identified. Of them, eight QTLs (qDA1_1, qGA1_1, qTIA1_1, qDA1_2, qGA1_2, qTIA1_2, qDA1_3, qTIA1_3) with phenotypic variation explained (PVE) ranging from 14.09 to 28.59% for daidzin, genistin, and total isoflavone were located on the same region of linkage group (LG) A1. These QTLs were further verified in another RIL population derived from Zheng 92116 × Qihuang 30 (ZQ). Meanwhile, the other four overlapping QTLs on linkage group B1, which were associated with glycitin content (qGLB1_1, qGLB1_2, qGLB1_3, qGLB1_4) and explained 16.52 to 29.83% of phenotypic variation, were also verified using the ZQ population. Moreover, the individuals with different genotypes at the common flanking SNP markers for these QTLs on LGs A1 and B1 in the two mapping populations showed significant different isoflavone content, which further validate the QTL mapping results. And also, some candidate genes might participate in the isoflavone biosynthesis processes were found in these stable QTL regions. Thus, the novel and stable QTLs identified and verified in this study could be applied in marker-assisted selection breeding or map-based candidate genes cloning in soybean seed isoflavone genetic improvement in future.