Mapping of quantitative trait loci for canopy-wilting trait in soybean (Glycine max L. Merr)

Drought stress adversely affects [Glycine max (L.) Merr] soybean at most developmental stages, which collectively results in yield reduction. Little information is available on relative contribution and chromosomal locations of quantitative trait loci (QTL) conditioning drought tolerance in soybean. A Japanese germplasm accession, PI 416937, was found to possess drought resistance. Under moisture-deficit conditions, PI 416937 wilted more slowly in the field than elite cultivars and has been used as a parent in breeding programs to improve soybean productivity. A recombinant inbred line (RIL) population was derived from a cross between PI 416937 and Benning, and the population was phenotyped for canopy wilting under rain-fed field conditions in five distinct environments to identify the QTL associated with the canopy-wilting trait. In a combined analysis over environments, seven QTL that explained 75?% of the variation in canopy-wilting trait were identified on different chromosomes, implying the complexity of this trait. Five QTL inherited their positive alleles from PI 416937. Surprisingly, the other two QTL inherited their positive alleles from Benning. These putative QTL were co-localized with other QTL previously identified as related to plant abiotic stresses in soybean, suggesting that canopy-wilting QTL may be associated with additional morpho-physiological traits in soybean. A locus on chromosome 12 (Gm12) from PI 416937 was detected in the combined analysis as well as in each individual environment, and explained 27?% of the variation in canopy-wilting. QTL identified in PI 416937 could provide an efficient means to augment field-oriented development of drought-tolerant soybean cultivars.     

Identification of QTL for increased fibrous roots in soybean

Drought stress adversely affects soybean at various developmental stages, which collectively results in yield reduction. Unpredictable rainfall has been reported to contribute about 36% to variation of yield difference between the rain-fed and irrigated fields. Among the drought resistance mechanisms, drought avoidance in genotypes with fibrous roots was recognized to be associated with drought resistance in soybean. Plant introduction PI416937 was shown to possess fibrous roots and has been used as a parent in breeding programs to improve soybean productivity. Little information is available on relative contribution and chromosomal location of quantitative trait loci (QTL) conditioning fibrous roots in soybean. To identify the genomic locations and genetic bases of this trait, a recombinant inbred line population was derived from a cross between PI416937 and ‘Benning’. To detect associated QTLs, phenotypic data were collected and analyzed for 2 years under rain-fed field conditions. The selective genotyping approach was used to reduce the costs and work associated with conducting the QTL analysis. A total of five QTLs were identified on chromosomes Gm01 (Satt383), Gm03 (Satt339), Gm04 (Sct_191), Gm08 (Satt429), and Gm20 (Sat_299), and together explained 51% of the variation in root score. Detected QTLs were co-localized with QTLs related to root morphology, suggesting that fibrous roots QTL may be associated with other morpho-physiological traits and seed yield in soybean. Genetic dissection of the fibrous roots trait at the individual marker loci will allow for marker-assisted selection to develop soybean genotypes with enhanced levels of fibrous roots.     

Identification of quantitative trait loci for bruchid (Caryedon serratus Olivier) resistance components in cultivated groundnut (Arachis hypogaea L.)

Groundnut bruchid (Caryedon serratus Olivier) is a major storage insect pest that significantly lowers the quality and market acceptance of the produce. Screening for resistance against groundnut bruchid in field conditions is difficult due to the variation in environmental factors and possible occurrence of biotypes. Hence, identification of tightly linked markers or quantitative trait loci (QTLs) is needed for selection and pyramiding of resistance genes for durable resistance. A population of recombinant inbred lines derived from a cross between VG 9514 (resistant) and TAG 24 (susceptible) was screened for five component traits of bruchid resistance in 2 years. The same population was genotyped with 221 polymorphic marker loci. A genetic linkage map covering 1,796.7 cM map distance was constructed with 190 marker loci in cultivated groundnut. QTL analysis detected thirteen main QTLs for four components of bruchid resistance in nine linkage groups and 31 epistatic QTLs for total developmental period (TDP). Screening in 2 years for bruchid resistance identified two common main QTLs. The common QTL for TDP, qTDP-b08, explained 57–82 % of phenotypic variation, while the other common QTL for adult emergence, qAE2010/11-a02, explained 13–21 % of phenotypic variation. Additionally, three QTLs for TDP, adult emergence and number of holes and one QTL for pod weight loss were identified which explained 14–39 % of phenotypic variation. This is the first report on identification of multiple main and epistatic loci for bruchid resistance in groundnut.     

Mapping soybean aphid resistance genes in PI 567598B

The soybean aphid (Aphis glycines Matsumura) has been a major pest of soybean [Glycine max (L.) Merr.] in North America since it was first reported in 2000. Our previous study revealed that the strong aphid resistance of plant introduction (PI) 567598B was controlled by two recessive genes. The objective of this study was to locate these two genes on the soybean genetic linkage map using molecular markers. A mapping population of 282 F_4:5 lines derived from IA2070 × E06902 was evaluated for aphid resistance in a field trial in 2009 and a greenhouse trial in 2010. Two quantitative trait loci (QTLs) were identified using the composite and multiple interval mapping methods, and were mapped on chromosomes 7 (linkage group M) and 16 (linkage group J), respectively. E06902, a parent derived from PI 567598B, conferred resistance at both loci. In the 2010 greenhouse trial, each of the two QTLs explained over 30 % of the phenotypic variation. Significant epistatic interaction was also found between these two QTLs. However, in the 2009 field trial, only the QTL on chromosome 16 was found and it explained 56.1 % of the phenotypic variation. These two QTLs and their interaction were confirmed with another population consisting of 94 F_2:5 lines in the 2008 and 2009 greenhouse trials. For both trials in the alternative population, these two loci explained about 50 and 80.4 % of the total phenotypic variation, respectively. Our study shows that soybean aphid isolate used in the 2009 field trial defeated the QTL found on chromosome 7. Presence of the QTL on chromosome 16 conferred soybean aphid resistance in all trials. The markers linked to the aphid-resistant QTLs in PI 567598B or its derived lines can be used in marker-assisted breeding for aphid resistance.     

QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance

Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be ‘adaptive’ to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.     

Identification of Major QTL for Waterlogging Tolerance Using Genome-Wide Association and Linkage Mapping of Maize Seedlings

To investigate the genetic basis of maize seedling response to waterlogging, we performed a genome-wide association study in 144 maize inbred lines, measuring length, fresh and dry weight of roots and shoots under normal and waterlogged conditions using 45,868 SNPs. This panel was divided into three subgroups based on the population structure results and the LD decay distance was 180 kb. A biparental advanced backcross (AB) population was also used to detect quantitative trait loci (QTL). In a comparison of 16 different models, principal components analysis (PCA/top PC3)?+?K was found to be best for reduction of false-positive associations for further analysis. A whole-genome scan detected four strong peak signals (P <?2.18?×?10^?5) significantly associated with the waterlogging response on chromosomes 5, 6 and 9. SNP4784, SNP200, SNP298, and SNP6314 showed significant association with corresponding traits under waterlogging and explained 14.99–19.36 %, 15.75–17.64 %, 16.08 % and 15.44 % of the phenotypic variation, respectively. The identified SNPs were located in GRMZM2G012046, GRMZM2G009808, GRMZM2G137108 and GRMZM2G369629 (AGPV1). SNP4784 (GRMZM2G012046) was colocalized with the major QTL that was identified with the same traits in the AB population. Forty-seven SNPs significantly associated (P?<?2.18?×?10^?4) with six traits in association mapping were identified and, among these, 33 SNPs were already reported in literature as waterlogging-related traits. These results will help elucidate the genetic basis of differential responses and tolerance to waterlogging stress among maize inbred lines, and provide novel loci for improvement of waterlogging tolerance of maize inbred lines using marker-assisted selection.     

Novel quantitative trait loci for partial resistance to Phytophthora sojae in soybean PI 398841

Phytophthora root and stem rot caused by Phytophthora sojae Kaufmann and Gerdemann is one of the most severe soybean [Glycine max (L.) Merr] diseases in the USA. Partial resistance is as effective in managing this disease as single-gene (Rps gene)-mediated resistance and is more durable. The objective of this study was to identify quantitative trait loci (QTL) associated with partial resistance to P. sojae in PI 398841, which originated from South Korea. A population of 305 F_7:8 recombinant inbred lines derived from a cross of OX20-8 × PI 398841 was used to evaluate partial resistance against P. sojae isolate C2S1 using a tray test. Composite interval mapping using a genome-wide logarithm of odd (LOD) threshold detected three QTL on chromosomes 1, 13, and 18, which individually explained 4–16 % of the phenotypic variance. Seven additional QTL, accounting for 2–3 % of phenotypic variance each, were identified using chromosome-wide LOD thresholds. Seven of the ten QTL for resistance to P. sojae were contributed by PI 398841. Seven QTL co-localized with known Rps genes and previously reported QTL for soil-borne root pathogens, isoflavone, and seed oil. Three QTL on chromosomes 3, 13, and 18 co-localized with known Rps genes, but PI 398841 did not exhibit an Rps gene-mediated resistance response following inoculation with 48 different isolates of P. sojae. PI 398841 is potentially a source of novel genes for improving soybean cultivars for partial resistance to P. sojae.     

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.     

Multiple loci associated with canine hip dysplasia (CHD) in German shepherd dogs

Canine hip dysplasia (CHD) is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we developed 37 informative single nucleotide polymorphisms (SNPs) within 13 quantitative trait loci (QTL) previously identified for German shepherd dogs. These SNPs were genotyped in 95 German shepherd dogs affected by CHD and 95 breed, sex, and birth year-matched controls. A total of ten SNPs significant at a nominal P value of 0.05 were validated in 843 German shepherd dogs including 277 unaffected dogs and 566 CHD-affected dogs. Cases and controls were sampled from the whole German shepherd dog population in Germany in such a way that mean coancestry coefficients were below 0.1 % within cases and controls as well as among cases and controls. We identified nine SNPs significantly associated with CHD within five QTL on dog chromosomes (CFA) 3, 9, 26, 33, and 34. Genotype effects of these nine SNPs explained between 22 and 34 % of the phenotypic variance of hip dysplasia in German shepherd dogs. The strongest associated SNPs were located on CFA33 and 34 within the candidate genes PNCP, TRIO, and SLC6A3. Thus, the present study validated positional candidate genes within five QTL for CHD.     

Linkage mapping and identification of QTL affecting deoxynivalenol (DON) content (Fusarium resistance) in oats (Avena sativa L.)

Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2–26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.     

Use of single nucleotide polymorphisms and haplotypes to identify genomic regions associated with protein content and water-soluble protein content in soybean

Key message

Four major SPC-specific loci were identified, and these accounted for 8.5–15.1 % of the phenotypic variation, thus explaining why certain soybean varieties have a high PC but a low SPC.

Abstract

Water-soluble protein content (SPC) is a critical factor in both food quality and the production of isolated soybean proteins. However, few data are available regarding the genetic control and the mechanisms contributing to elevated SPC. In this study, a soybean collection of 192 accessions from a wide geographic range was used to identify genomic regions associated with soybean protein content (PC) and SPC using an association mapping approach employing 1,536 SNP makers and 232 haplotypes. The diverse panel revealed a large genetic variation in PC and SPC. Association mapping was performed using three methods to minimize false-positive associations. This resulted in 4/8 SNPs and 3/6 haplotypes that were significantly associated with soybean PC/SPC in two or more environments based on the mixed model. An SNP that was highly significantly associated with PC, BARC-021267-04016, was localized 0.28 cM away from a published glycinin gene, G7, and was detected across all four environments. Four major SPC-specific loci, BARC-029149-06088, BARC-018023-02499, BARC-041663-08059 and haplotype 15 (hp15), were stably identified on chromosomes five and eight and explained 8.5–15.1 % of the phenotypic variation. Moreover, a glutelin type-B 2-like gene was identified on chromosome eight and may be related to soybean protein solubility. These markers, which are located in previously reported QTL, reconfirmed previous findings and may be important targets for the identification of protein-related genes. These novel SNPs and haplotypes are important for further understanding the genetic basis of PC and SPC. In addition, by comparing the correlation and genetic loci between PC and SPC, we provide new insights into why certain soybean varieties have a high protein content but a low SPC.     

QTL analysis of canning quality and color retention in black beans (Phaseolus vulgaris L.)

Black bean (Phaseolus vulgaris L.) consumption is increasing in the USA. One of the major challenges faced by breeders is to develop superior black bean cultivars to meet the demands of the canning industry. Processors require beans that take up water quickly during pre-canning soak and beans that retain their black color after canning. To properly assess canning quality requires expensive and detailed measurements of the canned product, often not possible for bean breeders. The objective of this research was identify quantitative trait loci (QTL) in a black bean recombinant inbred line (RIL) population for canning quality traits related to water uptake, color retention, and anthocyanin concentration. The parental lines from which the population was developed, Black Magic and Shiny Crow, contrasted in water uptake and color retention. These cultivars also differed in seed coat luster, controlled by a single gene, Asp. A medium-density linkage map of 1,449 markers and a distance of 1,660 cM was developed from this RIL population. The map was aligned to the bean genome sequence V1.0 by using sequence information associated with the Diversity Arrays Technology markers. QTL analysis revealed that the region near the Asp gene on chromosome Pv 07 is the major determinant of water uptake, explaining up to 49 % of the phenotypic variation. A group of QTL for color retention-related traits was found at the upper region of Pv 11, explaining up to 30 % of the phenotypic variation. A smaller effect QTL clustered on Pv 5 co-localized with a QTL for canned bean anthocyanin concentration and explained less than 10 % of the phenotypic variation. These color-related QTL have marker-assisted selection potential for bean breeders interested in enhancing color retention and anthocyanin concentration of processed black beans.     

Characterization of Yr54 and other genes associated with adult plant resistance to yellow rust and leaf rust in common wheat Quaiu 3

Leaf rust (LR) and yellow rust (YR), caused by Puccinia triticina and Puccinia striiformis f. sp. tritici, respectively, are important diseases of wheat. Quaiu 3, a common wheat line developed at the International Maize and Wheat Improvement Center (CIMMYT), is immune to YR in Mexico despite seedling susceptibility to predominant races. Quaiu 3 also shows immunity to LR in field trials and is known to possess the race-specific gene Lr42. A mapping population of 182 recombinant inbred lines (RILs) was developed by crossing Quaiu 3 with susceptible Avocet-YrA and phenotyped with LR and YR in field trials for 2 years in Mexico. Quantitative trait loci (QTL) associated with YR and LR resistance in the RILs were identified using Diversity Arrays Technology and simple sequence repeat markers. A large-effect QTL on the long arm of chromosome 2D explained 49–54 % of the phenotypic variation in Quaiu 3 and was designated as Yr54. Two additional loci on 1BL and 3BS explained 8–17 % of the phenotypic variation for YR and coincided with previously characterized adult plant resistance (APR) genes Lr46/Yr29 and Sr2/Yr30, respectively. QTL on 1DS and 1BL corresponding to Lr42 and Lr46/Yr29, respectively, contributed 60–71 % of the variation for LR resistance. A locus on 3D associated with APR to both diseases explained up to 7 % of the phenotypic variance. Additional Avocet-YrA-derived minor QTL were also detected for YR on chromosomes 1A, 3D, 4A, and 6A. Yr54 is a newly characterized APR gene which can be combined with other genes by using closely linked molecular markers.     

Mapping QTL for leaf area in oil palm using genotyping by sequencing

Leaf area is an important parameter in oil palm breeding as it is positively correlated with oil yield. However, measurement of leaf area is tedious and also destructive. In the present study, a breeding population with 145 palms derived from a cross between Deli Dura and Avros Pisifera was used to construct a high-density linkage map and identify quantitative trait loci (QTL) for leaf area in oil palm. Using genotyping by sequencing, a linkage map containing 2413 SNPs was constructed. The total length of the linkage map was 1161.89 cM, with an average marker spacing of 0.48 cM. Based on the continuous phenotyping of leaf area from 2010 to 2015, two suggestive QTL for leaf area were mapped on chromosomes (Chr) 3 and 9. The allelic effects of the QTL associated with leaf area in the mapping population were estimated by linear regression using ordinary least squares method. The QTL on Chr 9 explained 13.3% of phenotypic variation for leaf area. A candidate gene, ARC5, within the narrow interval of QTL on Chr 9 was identified. The gene was significantly higher expressed in leaf than root and fruit of oil palm. This high-quality and SNP-based map supplies a base to fine map QTL for agronomic traits in oil palm, and the markers closely linked to the stable QTL may be used in marker-assisted selection in oil palm breeding.     

Genetic mapping of a 7R Al tolerance QTL in triticale (x Triticosecale Wittmack)

Triticale (x Triticosecale Wittmack) is a relatively new cereal crop. In Poland, triticale is grown on 12 % of arable land (http://www.stat.gov.pl). There is an increasing interest in its cultivation due to lowered production costs and increased adaptation to adverse environmental conditions. However, it has an insufficient tolerance to the presence of aluminum ions (Al³⁺) in the soil. The number of genes controlling aluminum tolerance in triticale and their chromosomal location is not known. Two F2 mapping biparental populations (MP1 and MP15) segregating for aluminum (Al) tolerance were tested with AFLP, SSR, DArT, and specific PCR markers. Genetic mapping enabled the construction of linkage groups representing chromosomes 7R, 5R and 2B. Obtained linkage groups were common for both mapping populations and mostly included the same markers. Composite interval mapping (CIM) allowed identification of a single QTL that mapped to the 7R chromosome and explained 25 % (MP1) and 36 % (MP15) of phenotypic variation. The B1, B26 and Xscm150 markers were 0.04 cM and 0.02 cM from the maximum of the LOD function in the MP1 and MP15, respectively and were highly associated with aluminum tolerance as indicated by Kruskal–Wallis nonparametric test. Moreover, the molecular markers B1, B26, Xrems1162 and Xscm92, previously associated with the Alt4 locus that encoded an aluminum-activated malate transporter (ScALMT1) that was involved in Al tolerance in rye (Secale cereale) also mapped within QTL. Biochemical analysis of plants represented MP1 and MP15 mapping populations confirmed that the QTL located on 7R chromosome in both mapping populations is responsible for Al tolerance.     

Development of F1 hybrid population and the high-density linkage map for European aspen (<Emphasis Type="Italic">Populus tremula</Emphasis> L.) using RADseq technology

Background

Restriction-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.

Results

We 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.

Conclusions

The 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.

     

Mapping Quantitative Trait Loci for Omega-3 Fatty Acids in Asian Seabass

Omega-3 fatty acids are essential fatty acids for human health. Therefore, increasing both percentage of omega-3 and a better fatty acid profile in fish fillets is one of the breeding goals in aquaculture. However, it is difficult to increase the omega-3 content in fish fillets, as the phenotypic selection of these traits is not easily feasible. To facilitate the genetic improvement of the Asian seabass for optimal fatty acid profiles, a genome-wide scan for quantitative trait loci (QTL) affecting fatty acid level in the flesh of the Asian seabass was performed on an F₂ family containing 314 offspring. All family members were genotyped using 123 informative microsatellites and 22 SNPs. High percentages of n-3 polyunsaturated fatty acids (PUFA), especially C22:6 (DHA 16.48?±?3.09 %) and C20:5 (EPA 7.19?±?0.86 %) were detected in the flesh. One significant and 54 suggestive QTL for different fatty acids and a water content trait were detected on the whole genome. QTL for C18:0b was located on linkage groups (LG) 5. QTL for total n-3 PUFA content in flesh were mapped onto LG6 and LG23 with the phenotypic variance explained ranging from 3.8 to 6.3 %. Four QTL for C22:6 were detected on LG6, LG23, and LG24, explaining 3.9 to 4.9 % of the phenotypic variance, respectively. Mapping of QTL for contents of different fatty acids is the first step towards improving the omega-3 content in the fillets of fish by using marker-assisted selection and is important for understanding the biology of fatty acid deposition.     

Fine mapping of quantitative trait loci for acid phosphatase activity in maize leaf under low phosphorus stress

Acid phosphatase (APase) is very important in phosphorus (P) scavenging and remobilization in plants. The aim of this study was the fine mapping of quantitative trait loci (QTL) for APase activity (APA) in maize (Zea mays L.) leaf. The QTL for APA were studied in the F2:3 population derived from the cross 082 × Ye107 under low P stress in two sites. A significant difference in APA was found between 082 (P-efficient genotype) and Ye107 (P-deficient genotype). Each environment was analyzed to identify the QTL. Six QTL for APA were found, comprising two QTL at Beibei (BB) and four QTL at Hechuan (HC), China. A QTL denoted as AP9 showed a stable expression under different environments on chromosome 9, and explained 10.21 and 16.81 % of phenotypic variation at BB and HC, respectively. For the fine mapping of this QTL, seven individuals selected via marker-assisted selection in the BC3F1 population were used to produce the BC3F2 lines by selfing and to allow recombination within the region containing the target QTL. High-resolution genetic and physical maps were further constructed for the fine mapping of AP9 using 12 simple sequence repeat markers and the BC3F2 population consisting of 1,441 individuals. As a result, the location of AP9 was narrowed down to a 546-kb fragment on chromosome 9.     

Molecular mapping and inheritance of restoration of fertility (<Emphasis Type="Italic">Rf</Emphasis>) in A4 hybrid system in pigeonpea (<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millsp.)

Key message

We report molecular mapping and inheritance of restoration of fertility (Rf) in A4 hybrid system in pigeonpea. We have also developed PCR-based markers amenable to low-cost genotyping to identify fertility restorer lines.

Abstract

Commercial hybrids in pigeonpea are based on A4 cytoplasmic male sterility (CMS) system, and their fertility restoration is one of the key prerequisites for breeding. In this context, an effort has been made to understand the genetics and identify quantitative trait loci (QTL) associated with restoration of fertility (Rf). One F₂ population was developed by crossing CMS line (ICPA 2039) with fertility restorer line (ICPL 87119). Genetic analysis has shown involvement of two dominant genes in regulation of restoration of fertility. In parallel, the genotyping-by-sequencing (GBS) approach has generated ~?33 Gb data on the F₂ population. GBS data have provided 2457 single nucleotide polymorphism (SNPs) segregating across the mapping population. Based on these genotyping data, a genetic map has been developed with 306 SNPs covering a total length 981.9 cM. Further QTL analysis has provided the region flanked by S8_7664779 and S8_6474381 on CcLG08 harboured major QTL explained up to 28.5% phenotypic variation. Subsequently, sequence information within the major QTLs was compared between the maintainer and the restorer lines. From this sequence information, we have developed two PCR-based markers for identification of restorer lines from non-restorer lines and validated them on parental lines of hybrids as well as on another F₂ mapping population. The results obtained in this study are expected to enhance the efficiency of selection for the identification of restorer lines in hybrid breeding and may reduce traditional time-consuming phenotyping activities.