QTL mapping of potato chip color and tuber traits within an autotetraploid family

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid crop species, and this creates challenges for traditional line development and molecular breeding. Recent availability of a single-nucleotide polymorphism (SNP) array with 8303 features and software packages for linkage and association mapping in autotetraploid species present new opportunities for the identification of genomic regions that contribute to high-value traits in cultivated potato. A biparental tetraploid potato population was evaluated across three field seasons and storage trials in order to identify quantitative trait loci (QTL) for multiple tuber traits including fried chip color after 5.5–7.2 °C storage. Tetra-allelic dosage information was used to construct a genetic linkage map that covered 1041 cM and contained 2095 SNP markers with a median marker interval of 0.4 cM. A total of 41 QTL were identified for flower color, tuber yield, tuber number per plant, tuber weight, tuber size, and chip color after various storage regimes. Moderate effect QTL for chip color at 3 months were identified that co-localized with candidate genes vacuolar invertase (VInv), invertase inhibitor (INH2), and apoplastic invertase (Inv _ap -b). A separate QTL for chip color after 6 months of storage was identified in the short arm of chromosome 2, and this locus may contribute to variation in senescent sweetening resistance. QTL for tuber weight, length, and width co-localized with a known QTL for plant maturity on chromosome 5. Genome-wide association mapping using a polyploid model detected the tuber size QTL and identified a number of candidate SNPs, but was unable to detect markers significantly associated with chip color.     

Genetic analysis of net form net blotch resistance in barley lines CIho 5791 and Tifang against a global collection of <Emphasis Type="Italic">P. teres</Emphasis> f. <Emphasis Type="Italic">teres</Emphasis> isolates

Key message

A CIho 5791 × Tifang recombinant inbred mapping population was developed and used to identify major dominant resistance genes on barley chromosomes 6H and 3H in CI5791 and on 3H in Tifang.

Abstract

The barley line CIho 5791 confers high levels of resistance to Pyrenophora teres f. teres, causal agent of net form net blotch (NFNB), with few documented isolates overcoming this resistance. Tifang barley also harbors resistance to P. teres f. teres which was previously shown to localize to barley chromosome 3H. A CIho 5791 × Tifang F₆ recombinant inbred line (RIL) population was developed using single seed descent. The Illumina iSelect SNP platform was used to identify 2562 single nucleotide polymorphism (SNP) markers across the barley genome, resulting in seven linkage maps, one for each barley chromosome. The CIho 5791 × Tifang RIL population was evaluated for NFNB resistance using nine P. teres f. teres isolates collected globally. Tifang was resistant to four of the isolates tested whereas CIho 5791 was highly resistant to all nine isolates. QTL analysis indicated that the CIho 5791 resistance mapped to chromosome 6H whereas the Tifang resistance mapped to chromosome 3H. Additionally, CIho 5791 also harbored resistance to two Japanese isolates that mapped to a 3H region similar to that of Tifang. SNP markers and RILs harboring both 3H and 6H resistance will be useful in resistance breeding against NFNB.

     

Rapid identification of an adult plant stripe rust resistance gene in hexaploid wheat by high-throughput SNP array genotyping of pooled extremes

Key message

High-throughput SNP array analysis of pooled extreme phenotypes in a segregating population by KASP marker genotyping permitted rapid, cost-effective location of a stripe rust resistance QTL in wheat.

Abstract

German wheat cultivar “Friedrichswerther” has exhibited high levels of adult plant resistance (APR) to stripe rust in field environments for many years. F_2:3 lines and F₆ recombinant inbred line (RILs) populations derived from a cross between Friedrichswerther and susceptible landrace Mingxian 169 were evaluated in the field in 2013, 2016 and 2017. Illumina 90K iSelect SNP arrays were used to genotype bulked extreme pools and parents; 286 of 1135 polymorphic SNPs were identified on chromosome 6B. Kompetitive Allele-Specific PCR (KASP) markers were used to verify the chromosome region associated with the resistance locus. A linkage map was constructed with 18 KASP-SNP markers, and a major effect QTL was identified within a 1.4 cM interval flanked by KASP markers IWB71602 and IWB55937 in the region 6BL3-0-0.36. The QTL, named QYr.nwafu-6BL, was stable across environments, and explained average 54.4 and 47.8% of the total phenotypic variation in F_2:3 lines and F₆ RILs, respectively. On the basis of marker genotypes, pedigree analysis and relative genetic distance QYr.nwafu-6BL is likely to be a new APR QTL. Combined high-throughput SNP array genotyping of pooled extremes and validation by KASP assays lowers sequencing costs compared to genome-wide association studies with SNP arrays, and more importantly, permits rapid isolation of major effect QTL in hexaploid wheat as well as improving accuracy of mapping in the QTL region. QYr.nwafu-6BL with flanking KASP markers developed and verified in a subset of 236 diverse lines can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.

     

QTL mapping identifies a major locus for resistance in wheat to Sunn pest (<Emphasis Type="Italic">Eurygaster</Emphasis><Emphasis Type="Italic">integriceps</Emphasis>) feeding at the vegetative growth stage

Key message

This research provides the first report of a major locus controlling wheat resistance to Sunn pest. It developed and validated SNP markers that will be useful for marker-assisted selection.

Abstract

Sunn pest (Eurygaster integriceps Puton) is the most destructive insect pest of bread wheat and durum wheat in West and Central Asia and East Europe. Breeding for resistance at the vegetative stage of growth is vital in reducing the damage caused by overwintered adult populations that feed on shoot and leaves of seedlings, and in reducing the next generation of pest populations (nymphs and adults), which can cause damage to grain quality by feeding on spikes. In the present study, two doubled haploid (DH) populations involving resistant landraces from Afghanistan were genotyped with the 90k SNP iSelect assay and candidate gene-based KASP markers. The DH lines and parents were phenotyped for resistance to Sunn pest feeding, using artificial infestation cages at Terbol station, in Lebanon, over three years. Quantitative trait locus (QTL) analysis identified a single major locus on chromosome 4BS in the two populations, with the resistance allele derived from the landrace accessions, IG139431 and IG139883. The QTL explained a maximum of 42 % of the phenotypic variation in the Cham6 × IG139431 and 56 % in the Cham6 × IG139883 populations. SNP markers closest to the QTL showed high similarity to rice genes that putatively encode proteins for defense response to herbivory and wounding. The markers were validated in a large, unrelated population of parental wheat genotypes. All wheat lines carrying the ‘C–G’ haplotype at the identified SNPs were resistant, suggesting that selection based on a haplotype of favourable alleles would be effective in predicting resistance status of unknown genotypes.

     

Genetic mapping of quantitative trait loci for tuber-cadmium and zinc concentration in potato reveals associations with maturity and both overlapping and independent components of genetic control

Key message

Cd is a toxic metal, whilst Zn is an essential for plant and human health. Both can accumulate in potato tubers. We examine the genetic control of this process.

Abstract

The aim of this study was to map quantitative trait loci (QTLs) influencing tuber concentrations of cadmium (Cd) and zinc (Zn). We developed a segregating population comprising 188 F₁ progeny derived from crossing two tetraploid cultivars exhibiting divergent tuber-Cd-accumulation phenotypes. These progeny were genotyped using the SolCap 8303 SNP array, and evaluated for Cd, Zn, and maturity-related traits. Linkage and QTL mapping were performed using TetraploidSNPMap software, which incorporates all allele dosage information. The final genetic map comprised 3755 SNP markers with average marker density of 2.94 per cM. Tuber-Cd and Zn concentrations were measured in the segregating population over 2 years. QTL mapping identified four loci for tuber-Cd concentration on chromosomes 3, 5, 6, and 7, which explained genetic variance ranging from 5 to 33%, and five loci for tuber-Zn concentration on chromosome 1, 3, 5, and, 6 explaining from 5 to 38% of genetic variance. Among the QTL identified for tuber-Cd concentration, three loci coincided with tuber-Zn concentration. The largest effect QTL for both tuber-Cd and Zn concentration coincided with the maturity locus on chromosome 5 where earliness was associated with increased tuber concentration of both metals. Coincident minor-effect QTL for Cd and Zn sharing the same direction of effect was also found on chromosomes 3 and 6, and these were unrelated to maturity The results indicate partially overlapping genetic control of tuber-Cd and Zn concentration in the cross, involving both maturity-related and non-maturity-related mechanisms.

     

An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

Key message

We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL.

Abstract

Construction and use of linkage maps are challenging in hexaploids with polysomic inheritance. Full map integration requires calculations of recombination frequency between markers with complex segregation types. In addition, detection of QTL in hexaploids requires information on all six alleles at one locus for each individual. We describe a method that we used to construct a fully integrated linkage map for chrysanthemum (Chrysanthemum × morifolium, 2n = 6x = 54). A bi-parental F1 population of 406 individuals was genotyped with an 183,000 SNP genotyping array. The resulting linkage map consisted of 30,312 segregating SNP markers of all possible marker dosage types, representing nine chromosomal linkage groups and 107 out of 108 expected homologues. Synteny with lettuce (Lactuca sativa) showed local colinearity. Overall, it was high enough to number the chrysanthemum chromosomal linkage groups according to those in lettuce. We used the integrated and phased linkage map to reconstruct inheritance of parental haplotypes in the F1 population. Estimated probabilities for the parental haplotypes were used for multi-allelic QTL analyses on four traits with different underlying genetic architectures. This resulted in the identification of major QTL that were affected by multiple alleles having a differential effect on the phenotype. The presented linkage map sets a standard for future genetic mapping analyses in chrysanthemum and closely related species. Moreover, the described methods are a major step forward for linkage mapping and QTL analysis in hexaploids.

     

Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring

Key message

An integrated genetic map was constructed for einkorn wheat A genome and provided valuable information for QTL mapping and genome sequence anchoring.

Abstract

Wheat is one of the most widely grown food grain crops in the world. The construction of a genetic map is a key step to organize biologically or agronomically important traits along the chromosomes. In the present study, an integrated linkage map of einkorn wheat was developed using 109 recombinant inbred lines (RILs) derived from an inter sub-specific cross, KT1-1 (T. monococcum ssp. boeoticum) × KT3-5 (T. monococcum ssp. monococcum). The map contains 926 molecular markers assigned to seven linkage groups, and covers 1,377 cM with an average marker interval of 1.5 cM. A quantitative trait locus (QTL) analysis of five agronomic traits identified 16 stable QTL on all seven chromosomes, except 6A. The total phenotypic variance explained by these stable QTL using multiple regressions varied across environments from 8.8 to 87.1 % for days to heading, 24.4–63.0 % for spike length, 48.2–79.6 % for spikelet number per spike, 13.1–48.1 % for plant architecture, and 12.2–26.5 % for plant height, revealing that much of the RIL phenotypic variation had been genetically dissected. Co-localizations of closely linked QTL for different traits were frequently observed, especially on 3A and 7A. The QTL on 3A, 5A and 7A were closely associated with Eps-A ^m 3, Vrn1 and Vrn3 loci, respectively. Furthermore, this genetic map facilitated the anchoring of 237 T. urartu scaffolds onto seven chromosomes with a physical length of 26.15 Mb. This map and the QTL data provide valuable genetic information to dissect important agronomic and developmental traits in diploid wheat and contribute to the genetic ordering of the genome assembly.

     

Novel and major QTL for branch angle detected by using DH population from an exotic introgression in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Key message

A high-density SNP map was constructed and several novel QTL for branch angle across six environments in Brassica napus were identified.

Abstract

Branch angle is a major determinant for the ideotype of a plant, while the mechanisms underlying this trait in Brassica napus remain elusive. Herein, we developed one doubled haploid population from a cross involving one Capsella bursa-pastoris derived B. napus intertribal introgression line with the compressed branches and wooden stems, and constructed a high-density SNP map covering the genetic distance of 2242.14 cM, with an average marker interval of 0.73 cM. After phenotypic measurements across six environments, the inclusive composite interval mapping algorithm was conducted to analyze the QTL associated with branch angle. In single-environment analysis, a total of 17 QTL were detected and mainly distributed on chromosomes A01, A03, A09 and C03. Of these, three major QTL, qBA.A03-2, qBA.C03-3 and qBA.C03-4 were steadily expressed, each explaining more than 10% of the phenotypic variation in at least two environments. Compared with other results on rapeseed branch angle, these major QTL were newly detected. In QTL by environment interactions (QEI) mapping, 10 QTL were identified, and the QTL average effect and QEI effect were estimated. Of these, 7 QTL were detected in both single-environment analysis and QEI mapping. Based on the physical positions of SNPs and the functional annotation of the Arabidopsis thaliana genome, 27 genes within the QTL regions were selected as candidate genes, including early auxin-responsive genes, small auxin-up RNA, auxin/indoleacetic acid and gretchenhagen-3. These results may pave the way for deciphering the genetic control of branch angle in B. napus.

     

Association mapping of drought tolerance-related traits in barley to complement a traditional biparental QTL mapping study

Key message

Association mapping of drought-related traits in barley was used to increase the density of existing QTL maps without recreating mapping populations.

Abstract

We used 109 spring barley genotypes exhibiting high or low drought tolerance to elucidate the associations between diversity array technology sequencing (DArTseq) and single nucleotide polymorphism (SNP) markers and various physiological parameters related to plant responses to drought conditions. The study was performed in controlled conditions (growth chambers), drought tolerance was phenotyped in the four-leaf seedlings. We identified 58 associations including 34 new markers (i.e., 16 DArTseq and 18 SNP markers). The results for three markers were consistent with the data obtained in an earlier traditional biparental QTL mapping study. The regions neighboring markers on linkage group 2H contained the highest number of significant marker–trait associations. Five markers related to the photosynthetic activity of photosystem II were detected on chromosome 4H. The lowest number of associations were observed for the sequences neighboring DArT markers on linkage group 6H. A chromosome 3H region related to water use efficiency and net photosynthesis rate in both biparental QTL, and association study, may be particularly valuable, as these parameters correspond to the ability of plants to remain highly productive under water deficit stress. Our findings confirm that association mapping can increase the density of existing QTL maps without recreating mapping populations.

     

Identification of quantitative trait loci associated with resistance to net form net blotch in a collection of Nordic barley germplasm

Key message

Association mapping of resistance to Pyrenophora teres f. teres in a collection of Nordic barley germplasm at different developmental stages revealed 13 quantitative loci with mostly small effects.

Abstract

Net blotch, caused by the necrotrophic fungus Pyrenophora teres, is one of the major diseases in barley in Norway causing quantitative and qualitative yield losses. Resistance in Norwegian cultivars and germplasm is generally insufficient and resistance sources have not been extensively explored yet. In this study, we mapped quantitative trait loci (QTL) associated with resistance to net blotch in Nordic germplasm. We evaluated a collection of 209 mostly Nordic spring barley lines for reactions to net form net blotch (NFNB; Pyrenophora teres f. teres) in inoculations with three single conidia isolates at the seedling stage and in inoculated field trials at the adult stage in 4 years. Using 5669 SNP markers genotyped with the Illumina iSelect 9k Barley SNP Chip and a mixed linear model accounting for population structure and kinship, we found a total of 35 significant marker-trait associations for net blotch resistance, corresponding to 13 QTL, on all chromosomes. Out of these QTL, seven conferred resistance only in adult plants and four were only detectable in seedlings. Two QTL on chromosomes 3H and 6H were significant during both seedling inoculations and adult stage field trials. These are promising candidates for breeding programs using marker-assisted selection strategies. The results elucidate the genetic background of NFNB resistance in Nordic germplasm and suggest that NB resistance is conferred by a number of genes each with small-to-moderate effects, making it necessary to pyramid these genes to achieve sufficient levels of resistance.

     

Low validation rate of quantitative trait loci for Gibberella ear rot resistance in European maize

Key message

Six quantitative trait loci (QTL) for Gibberella ear rot resistance in maize were tested in two different genetic backgrounds; three QTL displayed an effect in few near isogenic line pairs.

Abstract

Few quantitative trait loci (QTL) mapping studies for Gibberella ear rot (GER) have been conducted, but no QTL have been verified so far. QTL validation is prudent before their implementation into marker-assisted selection (MAS) programs. Our objectives were to (1) validate six QTL for GER resistance, (2) evaluate the QTL across two genetic backgrounds, (3) investigate the genetic background outside the targeted introgressions. Pairs of near isogenic lines (NILs) segregating for a single QTL (Qger1, Qger2, Qger10, Qger13, Qger16, or Qger21) were developed by recurrent backcross until generation BC₃S₂. Donor parents (DP) carrying QTL were backcrossed to a susceptible (UH009) and a moderately resistant (UH007) recurrent parent. MAS was performed using five SNP markers covering a region of 40 cM around each QTL. All NILs were genotyped with the MaizeSNP50 assay and phenotyped for GER severity and deoxynivalenol and zearalenone content. Traits were significantly (P < 0.001) intercorrelated. Out of 34 NIL pairs with the UH009 genetic background, three pairs showed significant differences in at least one trait for three QTL (Qger1, Qger2, Qger13). Out of 25 NIL pairs with the UH007 genetic background, five pairs showed significant differences in at least one trait for two QTL (Qger2, Qger21). However, Qger16, Qger10 and Qger13 were most likely false positives. The genetic background possibly affected NIL pairs comparisons due to linkage drag and/or epistasis with residual loci from the DP in non-target regions. In conclusion, validation rates were disappointingly low, which further indicates that GER resistance is controlled by many low-effect QTL.

     

Combination of all-stage and high-temperature adult-plant resistance QTL confers high-level,durable resistance to stripe rust in winter wheat cultivar Madsen

Key message

Wheat cultivar Madsen has a new gene on the short arm of chromosome 1A and two QTL for all-stage resistance and three QTL for high-temperature adult-plant resistance that in combination confer high-level, durable resistance to stripe rust.

Abstract

Wheat cultivar Madsen has maintained a high-level resistance to stripe rust over 30 years. To map quantitative trait loci (QTL) underlying the high-level, durable resistance, 156 recombinant inbred lines (RILs) developed from cross Avocet S?×?Madsen were phenotyped with selected races of Puccinia striiformis f. sp. tritici in the greenhouse seedling tests, and in naturally infected fields during 2015–2017. The RILs were genotyped by SSR and SNP markers from genotyping by sequencing and the 90 K wheat SNP chip. Three QTL for all-stage resistance were mapped on chromosomes 1AS, 1BS and 2AS, and two QTL for high-temperature adult-plant (HTAP) resistance were mapped on 3BS and 6BS. The most effective QTL on 2AS, explaining 8.97–23.10% of the phenotypic variation in seedling tests and 8.60–71.23% in field tests, contained Yr17 for all-stage resistance and an additional gene for HTAP resistance. The 6BS QTL, detected in all field tests, was identified as Yr78. The 1AS QTL, conferring all-stage resistance, was identified as a new gene, which explained 20.45 and 30.23% of variation in resistance to races PSTv-37 and PSTv-40, respectively, and contributed significantly to field resistance at Pullman in 2015-2017, but was not detected at Mount Vernon. The interactions among QTL were mostly additive, and RILs with all five QTL had the highest level of resistance in the field, similar to Madsen. Genotyping 148 US Pacific Northwest wheat cultivars with markers for the 1AS, 2AS and 6BS QTL validated the genes and markers, and indicated their usefulness for marker-assisted selection.

     

The seed dormancy allele <Emphasis Type="Italic">TaSdr</Emphasis>-<Emphasis Type="Italic">A1a</Emphasis> associated with pre-harvest sprouting tolerance is mainly present in Chinese wheat landraces

Key message

We cloned TaSdr - A1 gene, and developed a gene-specific marker for TaSdr - A1 . A QTL for germination index at the TaSdr - A1 locus was identified in the Yangxiaomai/Zhongyou 9507 RIL population.

Abstract

Pre-harvest sprouting (PHS) affects yield and end-use quality in bread wheat (Triticum aestivum L.). In the present study we found an association between the TaSdr-A1 gene and PHS tolerance in bread wheat. TaSdr-A1 on chromosome 2A was cloned using a homologous cloning approach. Sequence analysis of TaSdr-A1 revealed an SNP at position 643, with the G allele being present in genotypes with lower germination index (GI) values and A in those with higher GI. These alleles were designated as TaSdr-A1a and TaSdr-A1b, respectively. A cleaved amplified polymorphism sequence (CAPS) marker Sdr2A based on the SNP was developed, and linkage mapping and QTL analysis were conducted to confirm the association between TaSdr-A1 and seed dormancy. Sdr2A was located in a 2.9 cM interval between SSR markers Xgwm95 and Xgwm372. A QTL for GI at the TaSdr-A1 locus explained 6.6, 7.3, and 8.2 % of the phenotypic variances in a Yangxiaomai/Zhongyou 9507 RIL population grown at Beijing, Shijiazhuang, and the averaged data from the two environments, respectively. Two sets of Chinese wheat cultivars used for validating the TaSdr-A1 polymorphism and the corresponding gene-specific marker Sdr2A showed that TaSdr-A1 was significantly associated with GI. Among 29 accessions with TaSdr-A1a, 24 (82.8 %) were landraces, indicating the importance of Chinese wheat landraces as sources of PHS tolerance. This study identified a novel PHS resistance allele TaSdr-A1a mainly presented in Chinese landraces and it is likely to be the causal gene for QPhs.ccsu-2A.3, providing new information for an understanding of seed dormancy.

     

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.)

Key message

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9.

Abstract

The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient ‘genetical genomics’ analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.     

Construction of a sequence-based bin map and mapping of QTLs for downy mildew resistance at four developmental stages in Chinese cabbage (<Emphasis Type="Italic">Brassica rapa</Emphasis> L. ssp. <Emphasis Type="Italic">pekinensis</Emphasis>)

Specific-locus amplified fragment sequencing is a high-resolution method for genetic mapping, genotyping, and single nucleotide polymorphism (SNP) marker discovery. Previously, a major QTL for downy mildew resistance, BraDM, was mapped to linkage group A08 in a doubled-haploid population derived from Chinese cabbage lines 91–112 and T12–19. The aim of the present study was to improve the linkage map and identify the genetic factors involved in downy mildew resistance. We detected 53,692 high quality SLAFs, of which 7230 were polymorphic, and 3482 of the polymorphic markers were used in genetic map construction. The final map included 1064 bins on ten linkage groups and was 858.98 cM in length, with an average inter-locus distance of 0.81 cM. We identified six QTLs that are involved in downy mildew resistance. The four major QTLs, sBrDM8, yBrDM8, rBrDM8, and hBrDM8, for resistance at the seedling, young plant, rosette, and heading stages were mapped to A08, and are identical to BraDM. The two minor resistance QTLs, rBrDM6 (A06) and hBrDM4 (A04), were active at the rosette and heading stages. The major QTL sBrDM8 defined a physical interval of ~228 Kb on A08, and a serine/threonine kinase family gene, Bra016457, was identified as the possible candidate gene. We report here the first high-density bin map for Chinese cabbage, which will facilitate mapping QTLs for economically important traits and SNP marker development. Our results also expand knowledge of downy mildew resistance in Chinese cabbage and provide three SNP markers (A08-709, A08-028, and A08-018) that we showed to be effective when used in MAS to breed for downy mildew resistance in B. rapa.     

Single nucleotide polymorphism tightly linked to a major QTL on chromosome 7A for both kernel length and kernel weight in wheat

Thousand-kernel weight (TKW) is one of the major components of grain yield in wheat (Triticum aestivum). Identifying major quantitative trait loci (QTLs) for TKW and developing effective markers are prerequisite for success in marker-assisted selection (MAS) to improve wheat yield through breeding. This study mapped a major QTL, designated as TaTKW-7AL, for increasing TKW on the long arm of chromosome 7A of ‘Clark’ to a 1.3-cM interval between single nucleotide polymorphism (SNP) markers IWB13913 and IWA5913. This QTL explained 19.7 % of the phenotypic variation for TKW. A QTL for increasing kernel length (KL), one of the major components of TKW, was mapped in the same interval as TaTKW-7AL, suggesting that increased TKW by the QTL in ‘Clark’ is most likely due to the increased KL. Association analysis on a diversity panel of 200 US winter wheat accessions also identified a haplotype of three SNP markers (IWB13913, IWB6693 and IWA5913) that were tightly associated with the both KL and TKW. The analysis of allele frequencies of the haplotype in the diversity panel suggested that the favorable allele of TaTKW-7AL has not been strongly selected for in practice and has potential to be used to improve grain yield in US hard winter wheat breeding. Two user-friendly flanking KASPar markers, IWB13913 and IWA5913, were developed for MAS of TaTKW-7AL.     

Genetic dissection of seed weight by QTL analysis and detection of allelic variation in Indian and east European gene pool lines of <Emphasis Type="Italic">Brassica juncea</Emphasis>

Key message

Seed weight QTL identified in different populations were synthesized into consensus QTL which were shown to harbor candidate genes by in silico mapping. Allelic variation inferred would be useful in breeding B. juncea lines with high seed weight.

Abstract

Seed weight is an important yield influencing trait in oilseed Brassicas and is a multigenic trait. Among the oilseed Brassicas, Brassica juncea harbors the maximum phenotypic variation wherein thousand seed weight varies from around 2.0 g to more than 7.0 g. In this study, we have undertaken quantitative trait locus/quantitative trait loci (QTL) analysis of seed weight in B. juncea using four bi-parental doubled-haploid populations. These four populations were derived from six lines (three Indian and three east European lines) with parental phenotypic values for thousand seed weight ranging from 2.0 to 7.6 g in different environments. Multi-environment QTL analysis of the four populations identified a total of 65 QTL ranging from 10 to 25 in each population. Meta-analysis of these component QTL of the four populations identified six ‘consensus’ QTL (C-QTL) in A3, A7, A10 and B3 by merging 33 of the 65 component Tsw QTL from different bi-parental populations. Allelic diversity analysis of these six C-QTL showed that Indian lines, Pusajaikisan and Varuna, hold the most positive allele in all the six C-QTL. In silico mapping of candidate genes with the consensus QTL localized 11 genes known to influence seed weight in Arabidopsis thaliana and also showed conserved crucifer blocks harboring seed weight QTL between the A subgenomes of B. juncea and B. rapa. These findings pave the way for a better understanding of the genetics of seed weight in the oilseed crop B. juncea and reveal the scope available for improvement of seed weight through marker-assisted breeding.

     

Mapping of <Emphasis Type="Italic">Sihc1</Emphasis>, which controls hull color,using a high-density genetic map based on restriction site-associated DNA sequencing in foxtail millet [<Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv.]

Hull color (HC) in foxtail millet appears to be a major indicator of nutritional quality. To attempt to identify and characterize the gene or quantitative trait locus (QTL) related to HC and to provide a basis for quality and yield breeding of foxtail millet, a restriction site-associated DNA sequencing (RAD-seq) analysis was employed to reveal genome-wide single nucleotide polymorphisms (SNPs) and to genotype the F₂ progeny from a cross between two cultivars: Heizhigu with green HC and Changnong 35 with yellow HC. A high-density linkage map spanning 1542.87 cM was constructed using 1694 bin markers, consisting of 46,256 SNP markers, and a QTL locus controlling HC was identified and temporarily named as Sihc1 (Setaria italica hull color). Results showed that Sihc1 was located in the interval between markers M33926512 and M34281352 on the end of chromosome 6, and explained 80.26% of the phenotypic variation with a logarithm of odds ratio of 93.46. The additive and dominant effects of Sihc1 were 1.0025 and ?0.9991, respectively. Sihc1 was narrowed to a 354.84 kb physical region, inclusive of 30 open reading frames, and further analysis suggested that Seita.6G226500, Seita.6G226800, Seita.6G228300, and Seita.6G228600 might be the key candidates of Sihc1.