The analysis of candidate genes and loci involved with carotenoid metabolism in cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz) using SLAF-seq

Carotenoids in cassava storage roots play important roles in benefiting people’s health in the tropics because they provide essential nutrients and antioxidants. Although the related genes and loci associated with carotenoid metabolism in many species are well reported, in cassava they are poorly understood. In the present study, GWAS base on SLAF-seq was used in detecting the related genes and loci correlated to carotenoid contents in 98 accessions from a cassava F₁ mapping population. The 98 accessions were divided into four subgroups. On the basis of general linear and compressed linear models, 144 genes were detected by selective sweep analysis, and 84 SNPs and 694 genes were detected by association mapping, in which Manes.04G164700 (XanDH) and Manes.11G105300 (AAO) were probably involved in the downstream pathway of carotenoid metabolism, and their expressions in six cassava genotypes were confirmed. Our results will be useful in yellow-root cassava variety improvement and provide the most effective and sustainable approach to maximize the nutritional and health benefits of carotenoid to a large number of populations.     

Interaction of quantitative trait loci for resistance to common bacterial blight and pathogen isolates in <Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.

Common bacterial blight (CBB) is a major disease of common bean (Phaseolus vulgaris L.) worldwide. Genetic resistance is the most effective and environmentally safe approach for controlling CBB, and identification of resistance quantitative trait loci (QTL) can improve response to selection when breeding for CBB resistance. Interactions of CBB resistance QTL and pathogen isolates with different levels of aggressiveness were studied using an F _4:5 recombinant inbreed line (RIL) population, derived from a cross between the susceptible cultivar “Sanilac” and the resistant breeding line “OAC 09-3.” Disease phenotyping was performed under field and growth room conditions using multiple bacterial isolates with differential levels of aggressiveness. QTL analysis was performed with 237 molecular markers. The effect of pathogen isolate on the average phenotypic value in the RIL population and the interaction of RILs and the pathogen isolates were highly significant. Two QTL underlying CBB resistance were detected on Pv08 and Pv03. A major QTL (R ² _p between 15 and 56%) was identified in a 5-cM (380 kbp) interval in the distal end of the long arm of Pv08. This genomic region was significantly associated with multiple disease evaluation traits in field and growth room assays and against different isolates of the pathogen, which included the previously known CBB marker SU91. A new QTL on Pv03 (Xa3.3^SO), associated with the PvSNP85p745405 allele from the susceptible parent, Sanilac, appeared to be an isolate-specific QTL against the aggressive fuscans isolate ISO118. Interaction between the SU91 and Xa3.3^SO QTL resulted in a significant reduction in mean disease severity for almost all disease evaluation traits after plants were challenged with the isolate ISO118. The 7.92 and 7.79% diseased areas in RILs with both QTL, compared with 14.92 and 13.81% in RILs without either in test1 and in test2 quantified by image analysis, showed a 44 and 47% reduction of percent diseased areas, indicating that the two QTL interact to limit the expansion of CBB symptoms after infection by ISO118. The information obtained in this study indicates that while the broad-spectrum SU91 QTL is useful in breeding programs, isolate-specific QTL, such as Xa3.3^SO, will aid in breeding bean varieties with enhanced resistance against aggressive regional isolates.     

Genetic analysis of shoot fresh weight in a cross of wild (<Emphasis Type="Italic">G. soja</Emphasis>) and cultivated (<Emphasis Type="Italic">G. max</Emphasis>) soybean

Shoot fresh weight (SFW) is one of the parameters, used to estimate the total plant biomass yield in soybean. In the present study, a total of 188 F_5:8 recombinant inbred lines (RIL) derived from an interspecific cross of PI 483463 (Glycine soja) and Hutcheson (Glycine max) were investigated for SFW variation in the field for three consecutive years. The parental lines and RILs were phenotyped in the field at the R6 stage by measuring total biomass in kg/plot to identify the QTLs for SFW. Three QTLs qSFW6_1, qSFW15_1, and qSFW19_1 influencing SFW were identified on chromosome 6, 15, and 19, respectively. The QTL qSFW19_1 flanked between the markers BARC-044913-08839 and BARC-029975-06765 was the stable QTL expressed in all the three environments. The phenotypic variation explained by the QTLs across all environments ranged from 6.56 to 21.32 %. The additive effects indicated contribution of alleles from both the parents and additive × environment interaction effects affected the expression of SFW QTL. Screening of the RIL population with additional SSRs from the qSFW19_1 region delimited the QTL between the markers SSR19-1329 and BARC-29975-06765. QTL mapping using bin map detected two QTLs, qSFW19_1A and qSFW19_1B. The QTL qSFW19_1A mapped close to the Dt1 gene locus, which affects stem termination, plant height, and floral initiation in soybean. Potential candidate genes for SFW were pinpointed, and sequence variations within their sequences were detected using high-quality whole-genome resequencing data. The findings in this study could be useful for understanding genetic basis of SFW in soybean.     

QTL analysis and the development of closely linked markers for days to flowering in spring oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Days to flowering (DTF) is an important trait impacting cultivar performance in oilseed rape (Brassica napus L.), but the interaction of all loci controlling this trait in spring-type oilseed rape is not fully understood. We identified quantitative trait loci (QTL) for variation in DTF in a doubled haploid (DH) population from the Qinghai–Tibet Plateau that includes 217 lines derived from a cross between spring-type oilseed rape (B. napus L.) line No. 5246 and line No. 4512, the latter of which is responsive to the effective accumulated temperature (EAT). A linkage map was constructed for the DH population, using 202 SSR and 293 AFLP markers. At least 22 DTF QTL were found in multiple environments. Four major QTL were located on linkage groups A7, C2, C8 and C8. Among these QTL, cqDTFA7a and cqDTFC2a were identified in five environments and individually explained 10.4 and 23.0 % of the trait variation, respectively. cqDTFC8, a major QTL observed in spring environments, and a unique winter environment QTL, qDTFC8-3, were identified; these QTL explained 10.0 and 46.5 % of the phenotypic variation, respectively. Minor QTL (for example, cqDTFC2c) and epistatic interactions seemed evident in this population. Two closely linked SSR markers for cqDTFA7a and cqDTFC8 were developed (G1803 and S034). BnAP1, a B. napus gene with homology to Arabidopsis thaliana that was identified as a cqDTFA7a candidate gene, played a major role in this study. The allelic effects of the major and minor QTL on DTF were further validated in the DH population and in 93 breeding genotypes.     

Genetic mapping of clubroot resistance genes in oilseed rape

Clubroot caused by the obligate biotrophic protist Plasmodiophora brassicae is a major disease of Brassica species. Clubroot resistances introduced from B. oleracea var. ‘Böhmerwaldkohl’ and resistance from B. rapa ECD-04 were genetically mapped in oilseed rape (B. napus L.). A doubled haploid (DH) population of rape seed was developed by crossing a resistant DH-line derived from a resynthesized B. napus with the susceptible cultivar ‘Express’. The DH population was tested in the greenhouse against seven P. brassicae isolates showing low and high virulence toward B. oleracea or/and B. rapa. DH-lines with highest or lowest disease scores were used in a bulked segregant analysis (BSA), and 43 polymorphic AFLPs were identified. A genetic map of the whole genome was constructed using 338 AFLP and 156 anchored SSR markers. Nineteen QTL were detected on chromosomes N02, N03, N08, N13, N15, N16 and N19 giving resistance to seven different isolates. Race-specific effects were observed for all QTL, none of the QTL conferred resistance to all isolates. The phenotypic variance explained by the respective QTL ranged between 10.3 and 67.5%. All QTL could be assigned to both ancestral genomes of B. napus. In contrast to previous reports, a clear differentiation into major QTL from B. rapa and minor QTL from B. oleracea could not be found. Composite interval mapping confirmed the linkage relationships determined by BSA, thus demonstrating that markers for oligogenic traits can be selected by merely testing the distributional extremes of a segregating population.     

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.

     

Identification of quantitative trait loci conferring resistance to tan spot in a biparental population derived from two Nebraska hard red winter wheat cultivars

Tan spot, caused by Pyrenophora tritici-repentis (Ptr), is a destructive foliar disease in all types of cultivated wheat worldwide. Genetics of tan spot resistance in wheat is complex, involving insensitivity to fungal-produced necrotrophic effectors (NEs), major resistance genes, and quantitative trait loci (QTL) conferring race-nonspecific and race-specific resistance. The Nebraska hard red winter wheat (HRWW) cultivar ‘Wesley’ is insensitive to Ptr ToxA and highly resistant to multiple Ptr races, but the genetics of resistance in this cultivar is unknown. In this study, we used a recombinant inbred line (RIL) population derived from a cross between Wesley and another Nebraska cultivar ‘Harry’ (Ptr ToxA sensitive and highly susceptible) to identify QTL associated with reaction to tan spot caused by multiple races/isolates. Sensitivity to Ptr ToxA conferred by the Tsn1 gene was mapped to chromosome 5B as expected. The Tsn1 locus was a major susceptibility QTL for the race 1 and race 2 isolates, but not for the race 2 isolate with the ToxA gene deleted. A second major susceptibility QTL was identified for all the Ptr ToxC-producing isolates and located to the distal end of the chromosome 1A, which likely corresponds to the Tsc1 locus. Three additional QTL with minor effects were identified on chromosomes 7A, 7B, and 7D. This work indicates that both Ptr ToxA-Tsn1 and Ptr ToxC-Tsc1 interactions are important for tan spot development in winter wheat, and Wesley is highly resistant largely due to the absence of the two tan spot sensitivity genes.     

Genome-wide characterization and stress-responsive expression profiling of <Emphasis Type="Italic">MCM</Emphasis> genes in <Emphasis Type="Italic">Brassica oleracea</Emphasis> and <Emphasis Type="Italic">Brassica rapa</Emphasis>

The Minichromosome maintenance protein [MCM (2-7)] complex is associated with helicase activity for replication fork formation during DNA replication. We identified and characterized each 12 putative MCM genes from Brassica oleracea and Brassica rapa. MCM genes were classified into nine groups according to their evolutionary relationships. A high number of syntenic regions were present on chromosomes C03 and A03 in B. oleracea and B. rapa, respectively, compared to the other chromosomes. Expression analysis showed that most of the MCM(2-7) helicase-subunit genes and their coregulating MCM genes were upregulated during hydroxyurea (HU) induced stress in B. oleracea. In B. rapa, MCM(2-7) helicase genes BrMCM2_2, BrMCM7_1, BrMCM7_2 and their co-regulating genes were upregulated during replication stress. During cold stress, BoMCM6 in B. oleracea and BrMCM5 in B. rapa were remarkably upregulated. During salt stress, BoMCM6_2, BoMCM7_1, BoMCM8, BoMCM9, and BoMCM10 were markedly upregulated in B. oleracea. Hence, our study identified the candidate MCM family genes those possess abiotic stress-responsive behavior and DNA replication stress tolerance. As the first genome-wide analysis of MCM genes in B. oleracea and B. rapa, this work provides a foundation to develop stress responsive plants. Further functional and molecular studies on MCM genes will be helpful to enhance stress tolerance in plants.     

The genetic architecture of seedling resistance to Septoria tritici blotch in the winter wheat doubled-haploid population Solitär × Mazurka

Breeding for resistance to Septoria tritici blotch (STB), caused by Mycosphaerella graminicola (anamorph: Septoria tritici), is an essential component in controlling this important foliar disease of wheat. Inheritance of seedling resistance to seven worldwide pathogen isolates has been studied in a doubled-haploid (DH) population derived from a cross between the field resistant cultivar Solitär and the susceptible cultivar Mazurka. Multiple quantitative trait locus (QTL) mapping revealed major and minor genetic effects on resistance as well as several epistatic relationships in the seedling stage. Solitär conferred resistance to isolate IPO323, governed by Stb6 on chromosome 3A, as well as to IPO99015, IPO92034, Hu1 and Hu2 controlled by a QTL on chromosome arm 1BS, possibly corresponding to Stb11 and minor QTL on chromosomes 1B, 3D, 6B and 7D. Resistance of Mazurka to IPO90015 and BBA22 was caused by a QTL located in a region on 4AL which harbours Stb7 or Stb12. QTL specific to pycnidial coverage on 3B and specific to necrosis on 1A could be discovered for isolate IPO92034. Pairwise epistatic interactions were reliably detected with five isolates. Although their contributions to the total variance are generally low, the genotypic effect of the QTL by QTL interaction of 4AL (Stb7 or Stb12) and 3AS (Stb6) made up almost 15% of disease expression. Altogether, the results suggest a complex inheritance of resistance to STB in the seedling stage in terms of isolate-specificity and resistance mechanisms, which have implications for marker-assisted breeding in an attempt to pyramid STB resistance genes.     

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.     

Genome-wide association study of heading and flowering dates and construction of its prediction equation in Chinese common wheat

Heading date is one of the most important traits in wheat breeding as it affects adaptation and yield potential. A genome-wide association study (GWAS) using the 90 K iSelect SNP genotyping assay indicated that a total of 306 loci were significantly associated with heading and flowering dates in 13 environments in Chinese common wheat from the Yellow and Huai wheat region. Of these, 105 loci were significantly correlated with both heading and flowering dates and were found in clusters on chromosomes 2, 5, 6, and 7. Based on differences in distribution of the vernalization and photoperiod genes among chromosomes, arms, or block regions, 13 novel, environmentally stable genetic loci were associated with heading and flowering dates, including RAC875_c41145_189 on 1DS, RAC875_c50422_299 on 2BL, and RAC875_c48703_148 on 2DS, that accounted for more than 20% phenotypic variance explained (PVE) of the heading/flowering date in at least four environments. GWAS and t test of a combination of SNPs and vernalization and photoperiod alleles indicated that the Vrn-B1, Vrn-D1, and Ppd-D1 genes significantly affect heading and flowering dates in Chinese common wheat. Based on the association of heading and flowering dates with the vernalization and photoperiod alleles at seven loci and three significant SNPs, optimal linear regression equations were established, which show that of the seven loci, the Ppd-D1 gene plays the most important role in modulating heading and flowering dates in Chinese wheat, followed by Vrn-B1 and Vrn-D1. Additionally, three novel genetic loci (RAC875_c41145_189, Excalibur_c60164_137, and RAC875_c50422_299) also show important effect on heading and flowering dates. Therefore, Ppd-D1, Vrn-B1, Vrn-D1, and the novel genetic loci should be further investigated in terms of improving heading and flowering dates in Chinese wheat. Further quantitative analysis of an F₁₀ recombinant inbred lines population identified a major QTL that controls heading and flowering dates within the Ppd-D1 locus with PVEs of 28.4% and 34.0%, respectively; this QTL was also significantly associated with spike length, peduncle length, fertile spikelets number, cold resistance, and tiller number.     

A novel allele of <Emphasis Type="Italic">TaGW2</Emphasis>-<Emphasis Type="Italic">A1</Emphasis> is located in a finely mapped QTL that increases grain weight but decreases grain number in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Key message

A novel TaGW2-A1 allele was identified from a stable, robust QTL region, which is pleiotropic for thousand grain weight, grain number per spike, and grain morphometric parameters in wheat.

Abstract

Thousand grain weight (TGW) and grain number per spike (GNS) are two crucial determinants of wheat spike yield, and genetic dissection of their relationships can help to fine-tune these two components and maximize grain yield. By evaluating 191 recombinant inbred lines in 11 field trials, we identified five genomic regions on chromosomes 1B, 3A, 3B, 5B, or 7A that solely influenced either TGW or GNS, and a further region on chromosome 6A that concurrently affected TGW and GNS. The QTL of interest on chromosome 6A, which was flanked by wsnp_BE490604A_Ta_2_1 and wsnp_RFL_Contig1340_448996 and designated as QTgw/Gns.cau-6A, was finely mapped to a genetic interval shorter than 0.538 cM using near isogenic lines (NILs). The elite NILs of QTgw/Gns.cau-6A increased TGW by 8.33%, but decreased GNS by 3.05% in six field trials. Grain Weight 2 (TaGW2-A1), a well-characterized gene that negatively regulates TGW and grain width in wheat, was located within the finely mapped interval of QTgw/Gns.cau-6A. A novel and rare TaGW2-A1 allele with a 114-bp deletion in the 5′ flanking region was identified in the parent with higher TGW, and it reduced TaGW2-A1 promoter activity and expression. In conclusion, these results expand our knowledge of the genetic and molecular basis of TGW-GNS trade-offs in wheat. The QTLs and the novel TaGW2-A1 allele are likely useful for the development of cultivars with higher TGW and/or higher GNS.

     

A genetic analysis of the quality of northern-style Chinese steamed bread

Dissecting the genetic basis for the traits of northern-style Chinese steamed bread (NCSB) is of great significance for wheat quality breeding. Quantitative trait loci (QTLs) for the processing quality of NCSB were studied using a recombinant inbred line (RIL) consisting of 173 lines derived from a “Shannong01–35 × Gaocheng9411” cross. Twenty-four putative additive QTLs were detected on chromosomes 1A, 1B, 1D, 3A, 3B, 4A, 4B, 5B, 6B, and 7B. Of these QTLs, QTex1A.1-27, QHei5B.5-488, and QGum4B.4-17 had the highest contribution and accounted for 9.33, 10.9, and 12.0% of the phenotypic variations, respectively. Several co-located QTLs with additive effects were detected on chromosomes 1A, 1D, 4B, and 5B. Two clusters (RFL_CONTIG2160_524-WSNP_CAP12_C2438_1180601 and EX_C101685_705-RAC875_C27536_611) for height, total score, and texture and for chewiness, gumminess, and hardness were detected on chromosomes 1A and 4B, respectively. Two QTLs for chewiness and hardness (QCh1D-4, QHa1D-4) with additive effects were detected; these alleles could be good targets for improving the processing quality of steamed bread from common wheat (Triticum aestivum L.). In addition, QTLs for wheat flour quality and the associated correlations with NCSB were simultaneously analyzed. Negative correlations were detected between chewiness and the wet/dry gluten content (WGC/DGC) or protein content. Two QTLs (QCh4B.4-17 and QPr4B.4-17) and three QTLs (QCh4B.4-13, QWG4B.4-13, and QDG4B.4-13) clustered in the same chromosomal region. The detected QTL clusters should be further investigated during wheat breeding and could be used by breeders to improve wheat quality and especially the processing quality of NCSB.     

QTL mapping of Fusarium head blight resistance in three related durum wheat populations

Key message

The QTL Fhb1 was successfully introgressed and validated in three durum wheat populations. The novel germplasm and the QTL detected will support improvement of Fusarium resistance in durum wheat.

Abstract

Durum wheat (Triticum durum Desf.) is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is hampered by limited genetic variation within this species. To date, resistant sources are mainly available in a few wild relative tetraploid wheat accessions. In this study, the effect of the well-known hexaploid wheat (Triticum aestivum L.) quantitative trait locus (QTL) Fhb1 was assessed for the first time in durum wheat. Three F7-RIL mapping populations of about 100 lines were developed from crosses between the durum wheat experimental line DBC-480, which carries an Fhb1 introgression from Sumai-3, and the European T. durum cultivars Karur, Durobonus and SZD1029K. The RILs were evaluated in field experiments for FHB resistance in three seasons using spray inoculation and genotyped with SSR as well as genotyping-by-sequencing markers. QTL associated with FHB resistance were identified on chromosome arms 2BL, 3BS, 4AL, 4BS, 5AL and 6AS at which the resistant parent DBC-480 contributed the positive alleles. The QTL on 3BS was detected in all three populations centered at the Fhb1 interval. The Rht-B1 locus governing plant height was found to have a strong effect in modulating FHB severity in all populations. The negative effect of the semi-dwarf allele Rht-B1b on FHB resistance was compensated by combining with Fhb1 and additional resistance QTL. The successful deployment of Fhb1 in T. durum was further substantiated by assessing type 2 resistance in one population. The efficient introgression of Fhb1 represents a significant step forward for enhancing FHB resistance in durum wheat.

     

Genetic analysis of genetic basis of a physiological disorder “straighthead” in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Straighthead is a physiological disorder in rice that causes yield losses and is a serious threat to rice production worldwide. Identification of QTL conferring resistance will help develop resistant cultivars for straighthead control. We conducted linkage mapping to identify QTL involved with straighthead. The study was based on a F₂ population developed from a cross between ‘Zhe733(resistant)/R312(susceptible)’. Using phenotypic data of F₂ plants and their F_2:3 families, two major QTL, qSTH-2 and qSTH-8, were identified using bulked segregant analysis, explaining 11.1 and 28.1 % of the phenotypic variation on chromosome 2 and 8, respectively. The qSTH-2 for straighthead resistance was identified by linkage mapping. qSTH-2 was situated near a QTL “AsS” responsible for arsenic accumulation. Straighthead is frequently observed on land where As has accumulated. The result suggests a kind of internal connection between qSTH-2 and AsS. Additionally, the QTL qSTH-8 was located close to HD5 related with heading date. The close location may be associated with the observation of early heading among straighthead resistant varieties. These findings should be useful for further genetic study of straighthead.     

QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population

Key message

Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized.

Abstract

The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line ‘Coolgreen’. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the ‘9930’ cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

     

Comparative genome-wide mapping versus extreme pool-genotyping and development of diagnostic SNP markers linked to QTL for adult plant resistance to stripe rust in common wheat

Key message

A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis.

Abstract

CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169?×?P10103. Five stable QTL were detected across multiple environments. After comparing SNP profiles from contrasting, extreme DNA pools of RILs six putative QTL were located to approximate chromosome positions. A major QTL on chromosome 4B was identified in F_2:4 contrasting pools from cross Zhengmai 9023?×?P10103. A consensus QTL (LOD?=?26–40, PVE?=?42–55%), named QYr.nwafu-4BL, was defined and localized to a 4.5-Mb interval flanked by SNP markers AX-110963704 and AX-110519862 in chromosome arm 4BL. Based on stripe rust response, marker genotypes, pedigree analysis and mapping data, QYr.nwafu-4BL is likely to be a new APR QTL. The applicability of the SNP-based markers flanking QYr.nwafu-4BL was validated on a diversity panel of 276 wheat lines. The additional minor QTL on chromosomes 4A, 5A, 5B and 6A enhanced the level of resistance conferred by QYr.nwafu-4BL. Marker-assisted pyramiding of QYr.nwafu-4BL and other favorable minor QTL in new wheat cultivars should improve the level of APR to stripe rust.

     

Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study

Key message

Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map.

Abstract

The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F_8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7-43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2-164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration.

     

High-resolution mapping of genes involved in plant stage-specific partial resistance of barley to leaf rust

Partial resistance quantitative trait loci (QTLs) Rphq11 and rphq16 against Puccinia hordei isolate 1.2.1 were previously mapped in seedlings of the mapping populations Steptoe/Morex and Oregon Wolfe Barleys, respectively. In this study, QTL mapping was performed at adult plant stage for the two mapping populations challenged with the same rust isolate. The results suggest that Rphq11 and rphq16 are effective only at seedling stage, and not at adult plant stage. The cloning of several genes responsible for partial resistance of barley to P. hordei will allow elucidation of the molecular basis of this type of plant defence. A map-based cloning approach requires to fine-map the QTL in a narrow genetic window. In this study, Rphq11 and rphq16 were fine-mapped using an approach aiming at speeding up the development of plant material and simplifying its evaluation. The plant materials for fine-mapping were identified from early plant materials developed to produce QTL-NILs. The material was first selected to carry the targeted QTL in heterozygous condition and susceptibility alleles at other resistance QTLs in homozygous condition. This strategy took four to five generations to obtain fixed QTL recombinants (i.e., homozygous resistant at the Rphq11 or rphq16 QTL alleles, homozygous susceptible at the non-targeted QTL alleles). In less than 2 years, Rphq11 was fine-mapped into a 0.2-cM genetic interval and a 1.4-cM genetic interval for rphq16. The strongest candidate gene for Rphq11 is a phospholipid hydroperoxide glutathione peroxidase. Thus far, no candidate gene was identified for rphq16.