Detection and Validation of QTL Affecting Bacterial Cold Water Disease Resistance in Rainbow Trout Using Restriction-Site Associated DNA Sequencing

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellite markers in a genome scan, we previously detected significant and suggestive QTL affecting phenotypic variation in survival following challenge with Flavobacterium psychrophilum, the causative agent of BCWD in rainbow trout. In this study, we performed selective genotyping of SNPs from restriction-site associated DNA (RAD) sequence data from two pedigreed families (2009070 and 2009196) to validate the major QTL from the previous work and to detect new QTL. The use of RAD SNPs in the genome scans increased the number of mapped markers from ~300 to ~5,000 per family. The significant QTL detected in the microsatellites scan on chromosome Omy8 in family 2009070 was validated explaining up to 58% of the phenotypic variance in that family, and in addition, a second QTL was also detected on Omy8. Two novel QTL on Omy11 and 14 were also detected, and the previously suggestive QTL on Omy1, 7 and 25 were also validated in family 2009070. In family 2009196, the microsatellite significant QTL on Omy6 and 12 were validated and a new QTL on Omy8 was detected, but none of the previously detected suggestive QTL were validated. The two Omy8 QTL from family 2009070 and the Omy12 QTL from family 2009196 were found to be co-localized with handling and confinement stress response QTL that our group has previously identified in a separate pedigreed family. With the currently available data we cannot determine if the co-localized QTL are the result of genes with pleiotropic effects or a mere physical proximity on the same chromosome segment. The genetic markers linked to BCWD resistance QTL were used to query the scaffolds of the rainbow trout reference genome assembly and the QTL-positive scaffold sequences were found to include 100 positional candidate genes. Several of the candidate genes located on or near the two Omy8 QTL detected in family 2009070 suggest potential linkages between stress response and the regulation of immune response in rainbow trout.     

Quantitative Trait Loci Affecting Response to Crowding Stress in an F2 Generation of Rainbow Trout Produced Through Phenotypic Selection

Selective breeding programs for salmonids typically aim to improve traits associated with growth and disease resistance. It has been established that stressors common to production environments can adversely affect these and other traits which are important to producers and consumers. Previously, we employed phenotypic selection to create families that exhibit high or low plasma cortisol concentrations in response to crowding stress. Subsequent crosses of high × low phenotypes founded a multigenerational breeding scheme with the aim of dissecting the genetic basis for variation underlying stress response through the identification of quantitative trait loci (QTL). Multiple methods of QTL analyses differing in their assumptions of homozygosity of the causal alleles in the grandparental generation yielded similar results in the F₁ generation, and the analysis of two stress response phenotype measurement indexes were highly correlated. In the current study, we conducted a genome scan with microsatellites to detect QTL in the F₂ generation of two families created through phenotypic selection and having larger numbers of offspring than families screened in the previous generation. Seven suggestive and three significant QTL were detected, seven of which were not previously detected in the National Center for Cool and Cold Water Aquaculture germplasm, bringing the total number of chromosomes containing significant and suggestive stress response QTL to 4 and 15, respectively. One significant QTL which peaks at 7 cM on chromosome Omy12 spans 12 cM and explains 25 % of the phenotypic variance in family 2008052 particularly warrants further investigation. Five QTL with significant parent-of-origin effects were detected in family 2008052, including two QTL on Omy12. The 95 % confidence intervals for the remaining QTL we detected were broad, requiring validation and fine mapping with other genotyping approaches and mapping strategies. These results will facilitate identification of potential casual alleles that can be employed in strategies aimed at better understanding the genetic and physiological basis of stress responses to crowding in rainbow trout aquaculture production.     

Assessment of Genetic Correlation between Bacterial Cold Water Disease Resistance and Spleen Index in a Domesticated Population of Rainbow Trout: Identification of QTL on Chromosome Omy19

Selective breeding of animals for increased disease resistance is an effective strategy to reduce mortality in aquaculture. However, implementation of selective breeding programs is limited by an incomplete understanding of host resistance traits. We previously reported results of a rainbow trout selection program that demonstrated increased survival following challenge with Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). Mechanistic study of disease resistance identified a positive phenotypic correlation between post-challenge survival and spleen somatic-index (SI). Herein, we investigated the hypothesis of a genetic correlation between the two traits influenced by colocalizing QTL. We evaluated the inheritance and calculated the genetic correlation in five year-classes of odd- and even-year breeding lines. A total of 322 pedigreed families (n = 25,369 fish) were measured for disease resistance, and 251 families (n = 5,645 fish) were evaluated for SI. Spleen index was moderately heritable in both even-year (h² = 0.56±0.18) and odd-year (h² = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (r_g = 0.45±0.20, P = 0.03) but not in the odd-year line (r_g = 0.16±0.12, P = 0.19). Complex segregation analyses of the even-year line provided evidence of genes with major effect on SI, and a genome scan of a single family, 2008132, detected three significant QTL on chromosomes Omy19, 16 and 5, in addition to ten suggestive QTL. A separate chromosome scan for disease resistance in family 2008132 identified a significant BCWD QTL on Omy19 that was associated with time to death and percent survival. In family 2008132, Omy19 microsatellite alleles that associated with higher disease resistance also associated with increased spleen size raising the hypothesis that closely linked QTL contribute to the correlation between these traits. To our knowledge, this is the first estimation of spleen size heritability and evidence for genetic linkage with specific disease resistance in a teleost fish.     

Construction of high-density linkage map and identification of QTLs for resistance to sorghum downy mildew in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

Sorghum downy mildew (SDM), caused by obligate biotrophic fungi Peronosclerospora sorghi, is an economically important disease of maize. The genetics of resistance was reported to be polygenic thereby necessitating identification of QTLs for resistance to SDM to initiate effective marker-assisted selection programs. During post-rainy and winter season of 2012, 645 F_2:3 progeny families from the cross CML153 (susceptible) × CML226 (resistant) were screened for their reaction to SDM. Characterization of QTLs affecting resistance to SDM was undertaken using the genetic linkage map with 319 polymorphic SSR and SNP marker loci and the phenotypic data of F_2:3 families. Three QTLs conferring resistance to SDM were consistently identified on chromosomes 2, 3 and 6 in both seasons. The resistant parent CML226 contributed all the QTL alleles conferring resistance to SDM. The major QTL located on chromosome 2 explained 38.68% of total phenotypic variation in the combined analysis with a LOD score of 9.12. All the three QTL showed partially dominant gene effects in combined analysis. The detection of more than one QTL supports the hypothesis that quantitative genes control resistance to P. sorghi. The generation was advanced to F₆ using markers linked to major QTLs on chromosomes 2 and 3 to derive 33 SDM resistant maize inbred lines.     

Fine mapping of a preharvest sprouting QTL interval on chromosome 2B in white wheat

Key message

Fine mapping by recombinant backcross populations revealed that a preharvest sprouting QTL on 2B contained two QTLs linked in coupling with different effects on the phenotype.

Abstract

Wheat preharvest sprouting (PHS) occurs when grain germinates on the plant before harvest, resulting in reduced grain quality. Previous mapping of quantitative trait locus (QTL) revealed a major PHS QTL, QPhs.cnl-2B.1, located on chromosome 2B significant in 16 environments that explained from 5 to 31 % of the phenotypic variation. The objective of this project was to fine map the QPhs.cnl-2B.1 interval. Fine mapping was carried out in recombinant backcross populations (BC₁F₄ and BC₁F₅) that were developed by backcrossing selected doubled haploids to a recurrent parent and self-pollinating the BC₁F₄ and BC₁F₅ generations. In each generation, three markers in the QPhs.cnl-2B.1 interval were used to screen for recombinants. Fine mapping revealed that the QPhs.cnl-2B.1 interval contained two PHS QTLs linked in coupling. The distal PHS QTL, located between Wmc453c and Barc55, contributed 8 % of the phenotypic variation and also co-located with a major seed dormancy QTL determined by germination index. The proximal PHS QTL, between Wmc474 and CNL415-rCDPK, contributed 16 % of the variation. Several candidate genes including Mg-chelatase H subunit family protein, GTP-binding protein and calmodulin/Ca²⁺-dependent protein kinase were linked to the PHS QTL. Although many recombinant lines were identified, the lack of polymorphism for markers in the QTL interval prevented the localization of the recombination breakpoints and identification of the gene underlying the phenotype.     

Identification of Novel QTLs for Isolate-Specific Partial Resistance to Plasmodiophora brassicae in Brassica rapa

Plasmodiophora brassicae, the causal agent of clubroot disease of the Brassica crops, is widespread in the world. Quantitative trait loci (QTLs) for partial resistance to 4 different isolates of P. brassicae (Pb2, Pb4, Pb7, and Pb10) were investigated using a BC₁F₁ population from a cross between two subspecies of Brassica rapa, i.e. Chinese cabbage inbred line C59-1 as a susceptible recurrent parent and turnip inbred line ECD04 as a resistant donor parent. The BC₁F₂ families were assessed for resistance under controlled conditions. A linkage map constructed with simple sequence repeats (SSR), unigene-derived microsatellite (UGMS) markers, and specific markers linked to published clubroot resistance (CR) genes of B. rapa was used to perform QTL mapping. A total of 6 QTLs residing in 5 CR QTL regions of the B. rapa chromosomes A01, A03, and A08 were identified to account for 12.2 to 35.2% of the phenotypic variance. Two QTL regions were found to be novel except for 3 QTLs in the respective regions of previously identified Crr1, Crr2, and Crr3. QTL mapping results indicated that 1 QTL region was common for partial resistance to the 2 isolates of Pb2 and Pb7, whereas the others were specific for each isolate. Additionally, synteny analysis between B. rapa and Arabidopsis thaliana revealed that all CR QTL regions were aligned to a single conserved crucifer blocks (U, F, and R) on 3 Arabidopsis chromosomes where 2 CR QTLs were detected in A. thaliana. These results suggest that some common ancestral genomic regions were involved in the evolution of CR genes in B. rapa.     

QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L.)

Powdery mildew (PM) is a very important disease of cucumber (Cucumis sativus L.). Resistant cultivars have been deployed in production for a long time, but the genetic mechanisms of PM resistance in cucumber are not well understood. A 3-year QTL mapping study of PM resistance was conducted with 132 F_2:3 families derived from two cucumber inbred lines WI 2757 (resistant) and True Lemon (susceptible). A genetic map covering 610.4 cM in seven linkage groups was developed with 240 SSR marker loci. Multiple QTL mapping analysis of molecular marker data and disease index of the hypocotyl, cotyledon and true leaf for responses to PM inoculation identified six genomic regions in four chromosomes harboring QTL for PM resistance in WI 2757. Among the six QTL, pm1.1 and pm1.2 in chromosome 1 conferred leaf resistance. Minor QTL pm3.1 (chromosome 3) and pm4.1 (chromosome 4) contributed to disease susceptibility. The two major QTL, pm5.1 and pm5.2 were located in an interval of ~40 cM in chromosome 5 with each explaining 21.0–74.5 % phenotypic variations. Data presented herein support two recessively inherited, linked major QTL in chromosome 5 plus minor QTL in other chromosomes that control the PM resistance in WI 2757. The QTL pm5.2 for hypocotyl resistance plays the most important role in host resistance. Multiple observations in the same year revealed the importance of scoring time in the detection of PM resistance QTL. Results of this study provided new insights into phenotypic and genetic mechanisms of powdery mildew resistance in cucumber.     

Mapping of the quantitative trait locus (QTL) conferring partial resistance to rice leaf blast disease

Malaysian rice, Pongsu Seribu 2, has wide-spectrum resistance against blast disease. Chromosomal locations conferring quantitative resistance were detected by linkage mapping with SSRs and quantitative trait locus (QTL) analysis. For the mapping population, 188 F₃ families were derived from a cross between the susceptible cultivar, Mahsuri, and a resistant variety, Pongsu Seribu 2. Partial resistance to leaf blast in the mapping population was assessed. A linkage map covering ten chromosomes and consisting of 63 SSR markers was constructed. 13 QTLs, including 6 putative and 7 putative QTLs, were detected on chromosomes 1, 2, 3, 5, 6, 10, 11 and 12. The resulting phenotypic variation due to a single QTL ranged from 2 to 13 %. These QTLs accounted for approx. 80 % of the total phenotypic variation within the F₃ population. Therefore, partial resistance to blast in Pongsu Seribu 2 is due to combined effects of multiple loci with major and minor effects.     

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

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

Mapping quantitative trait loci associated with regeneration ability of seed callus in rice, Oryza sativa L.

 Quantitative trait loci (QTL) controlling the regeneration ability of rice seed callus were detected using 245 RFLP markers and 98 BC₁F₅ lines derived from two varieties, ‘Nipponbare’ and ‘Kasalath’. Regeneration ability was evaluated by two indices: average number of regenerated shoots per callus (NRS) and regeneration rate (RR). The BC₁F₅ lines showed continuous segregation for both indices. Five putative QTL for NRS (tentatively named qRg1, qRg2, qRg4a, qRg4b and qRg4c) located on chromosomes 1, 2 and 4 were detected. Digenic interaction among these detected QTL was not significant (P<0.01). Among the five QTL detected, four ‘Kasalath’ alleles and one ‘Nipponbare’ allele increased NRS. According to an estimate based on the nearest marker loci, the five QTL accounted for 38.5% of the total phenotypic variation of the BC₁F₅ lines. For RR, four putative QTL were detected on chromosomes 2 and 4, and all of these were in the same chromosomal regions as the NRS QTL. The four RR QTL accounted for 32.6% of the total phenotypic variation. Received: 7 November 1996 / Accepted: 25 April 1997     

A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss)

Whirling disease, caused by the pathogen Myxobolus cerebralis, leads to skeletal deformation, neurological impairment and under certain conditions, mortality of juvenile salmonid fishes. The disease has impacted the propagation and survival of many salmonid species over six continents, with particularly negative consequences for rainbow trout. To assess the genetic basis of whirling disease resistance in rainbow trout, genome-wide mapping was initiated using a large outbred F(2) rainbow trout family (n=480) and results were confirmed in three additional outbred F(2) families (n=96 per family). A single quantitative trait locus (QTL) region on chromosome Omy9 was identified in the large mapping family and confirmed in all additional families. This region explains 50-86% of the phenotypic variance across families. Therefore, these data establish that a single QTL region is capable of explaining a large percentage of the phenotypic variance contributing to whirling disease resistance. This is the first genetic region discovered that contributes directly to the whirling disease phenotype and the finding moves the field closer to a mechanistic understanding of resistance to this important disease of salmonid fish.     

Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219

A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC₂F₂ population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16.2?cM, spanning 1,553.4?cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3.0). The O. rufipogon allele was favourable for 59% of QTLs detected through CIM. Of 261 BC₂F₂ families, 26 advanced backcross breeding lines (BC₂F₅) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC₂F₃ and BC₂F₄ generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC₂F₅ generation whereas 29 QTLs were detected in BC₂F₂ generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R ² values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC₂F₅ population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization.     

Mapping QTL controlling maize deep-seeding tolerance-related traits and confirmation of a major QTL for mesocotyl length

Deep-seeding tolerant seeds can emerge from deep soil where the moisture is suitable for seed germination. Breeding deep-seeding tolerant cultivars is becoming increasingly important in arid and semi-arid regions. To dissect the quantitative trait loci (QTL) controlling deep-seeding tolerance traits, we selected a tolerant maize inbred line 3681-4 and crossed it with the elite inbred line-X178 to generate an F₂ population and the derivative F_2:3 families. A molecular linkage map composed of 179 molecular markers was constructed, and 25 QTL were detected including 10 QTL for sowing at 10 cm depth and 15 QTL for sowing at 20 cm depth. The QTL analysis results confirmed that deep-seeding tolerance was mainly caused by mesocotyl elongation and also revealed considerable overlap among QTL for different traits. To confirm a major QTL on chromosome 10 for mesocotyl length measured at 20 cm depth, we selected and self-pollinated a BC₃F₂ plant that was heterozygous at the markers around the target QTL and homozygous at other QTL to generate a BC₃F₃ population. We found that this QTL explained more phenotypic variance in the BC₃F₃ population than that in the F₂ population, which laid the foundation for fine mapping and NIL (near-isogenic line) construction.     

Dissecting quantitative resistance against blast disease using heterogeneous inbred family lines in rice

SHZ-2 is an indica rice cultivar that exhibits broad-spectrum resistance to rice blast; it is widely used as a resistance donor in breeding programs. To dissect the QTL responsible for broad-spectrum blast resistance, we crossed SHZ-2 to TXZ-13, a blast susceptible indica variety, to produce 244 BC₄F₃ lines. These lines were evaluated for blast resistance in greenhouse and field conditions. Chromosomal introgressions from SHZ-2 into the TXZ-13 genome were identified using a single feature polymorphism microarray, SSR markers and gene-specific primers. Segregation analysis of the BC₄F₃ population indicated that three regions on chromosomes 2, 6, and 9, designated as qBR2.1, qBR6.1, and qBR9.1, respectively, was associated with blast resistance and contributed 16.2, 14.9, and 22.3%, respectively, to the phenotypic variance of diseased leaf area (DLA). We further narrowed the three QTL regions using pairs of sister lines extracted from heterogeneous inbred families (HIF). Pairwise comparison of these lines enabled the determination of the relative contributions of individual QTL. The qBR9.1 conferred strong resistance, whereas qBR2.1 or qBR6.1 individually did not reduce disease under field conditions. However, when qBR2.1 and qBR6.1 were combined, they reduced disease by 19.5%, suggesting that small effect QTLs contribute to reduction of epidemics. The qBR6.1 and qBR9.1 regions contain nucleotide-binding sites and leucine rich repeats (NBS-LRR) sequences, whereas the qBR2.1 did not. In the qBR6.1 region, the patterns of expression of adjacent NBS-LRR genes were consistent in backcross generations and correlated with blast resistance, supporting the hypothesis that multiple resistance genes within a QTL region can contribute to non-race-specific quantitative resistance.     

Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines

 To detect quantitative trait loci (QTLs) controlling seed dormancy, 98 BC₁F₅ lines (backcross inbred lines) derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare were analyzed genetically. We used 245 RFLP markers to construct a framework linkage map. Five putative QTLs affecting seed dormancy were detected on chromosomes 3, 5, 7 (two regions) and 8, respectively. Phenotypic variations explained by each QTL ranged from 6.7% to 22.5% and the five putative QTLs explained about 48% of the total phenotypic variation in the BC₁F₅ lines. Except for those of the QTLs on chromosome 8, the Nipponbare alleles increased the germination rate. Five putative QTLs controlling heading date were detected on chromosomes 2, 3, 4, 6 and 7, respectively. The phenotypic variation explained by each QTL for heading date ranged from 5.7% to 23.4% and the five putative QTLs explained about 52% of the total phenotypic variation. The Nipponbare alleles increased the number of days to heading, except for those of two QTLs on chromosomes 2 and 3. The map location of a putative QTL for heading date coincided with that of a major QTL for seed dormancy on chromosome 3, although two major heading-date QTLs did not coincide with any seed dormancy QTLs detected in this study. Received: 10 October 1997 / Accepted: 12 January 1998     

Mapping of QTL for Fusarium head blight resistance and morphological and developmental traits in three backcross populations derived from Triticum dicoccum?×?Triticum durum

Breeding for resistance to Fusarium head blight (FHB) in durum wheat continues to be hindered by the lack of effective resistance sources. Only limited information is available on resistance QTL for FHB in tetraploid wheat. In this study, resistance to FHB of a Triticum dicoccum line in the background of three Austrian T. durum cultivars was genetically characterized. Three populations of BC₁F₄-derived RILs were developed from crosses between the resistant donor line T. dicoccum-161 and the Austrian T. durum recipient varieties DS-131621, Floradur and Helidur. About 130 BC₁F₄-derived lines per population were evaluated for FHB response using artificial spray inoculation in four field experiments during two seasons. Lines were genetically fingerprinted using SSR and AFLP markers. Genomic regions on chromosomes 3B, 4B, 6A, 6B and 7B were significantly associated with FHB severity. FHB resistance QTL on 6B and 7B were identified in two populations and a resistance QTL on 4B appeared in three populations. The alleles that enhanced FHB resistance were derived from the T. dicoccum parent, except for the QTL on chromosome 3B. All QTL except the QTL on 6A mapped to genomic regions where QTL for FHB have previously been reported in hexaploid wheat. QTL on 3B and 6B coincided with Fhb1 and Fhb2, respectively. This implies that tetraploid and hexaploid wheat share common genomic regions associated with FHB resistance. QTL for FHB resistance on 4B co-located with a major QTL for plant height and mapped at the position of the Rht-B1 gene, while QTL on 7B overlapped with QTL for flowering time.     

Molecular cytogenetic identification of B genome chromosomes linked to blackleg disease resistance in Brassica napus × B. carinata interspecific hybrids

Key message

Provide evidence that the Brassica B genome chromosome B3 carries blackleg resistance gene, and also the B genome chromosomes were inherited several generations along with B. napus chromosomes.

Abstract

Blackleg disease caused by fungus Leptosphaeria maculans causes significant yield losses in Brassica napus. Brassica carinata possesses excellent resistance to this disease. To introgress blackleg resistance, crosses between B. napus cv. Westar and B. carinata were done. The interspecific-hybrids were backcrossed twice to Westar and self-pollinated three times to produce BC₂S₃ families. Doubled haploid lines (DH1) were produced from one blackleg resistant family. SSR markers were used to study the association between B genome chromosome(s) and blackleg resistance. The entire B3 chromosome of B. carinata was associated with blackleg resistance in DH1. A second DH population (DH2) was produced from F₁s of resistant DH1 lines crossed to blackleg susceptible B. napus cv. Polo where resistance was found to be associated with SSR markers from the middle to bottom of the B3 and top of the B8 chromosomes. The results demonstrated that the B3 chromosome carried gene(s) for blackleg resistance. Genomic in situ hybridization (GISH) and GISH-like analysis of the DH2 lines revealed that susceptible lines, in addition to B. napus chromosomes, possessed one pair of B genome chromosomes (2n = 40), while resistant lines had either one (2n = 40) or two pairs (2n = 42) of B chromosomes. The molecular and GISH data suggested that the B chromosome in the susceptible lines was B7, while it was difficult to confirm the identity of the B chromosomes in the resistant lines. Also, B chromosomes were found to be inherited over several generations along with B. napus chromosomes.     

Identification and fine-mapping of a major QTL conferring resistance against head smut in maize

Head smut is one of the most devastating diseases in maize, causing severe yield loss worldwide. Here we report identification and fine-mapping of a major quantitative trait locus (QTL) conferring resistance to head smut. Two inbred lines ‘Ji1037’ (donor parent, highly resistant) and ‘Huangzao4’ (recurrent parent, highly susceptible) were crossed and then backcrossed to ‘Huangzao4’ to generate BC populations. Four putative resistance QTLs were detected in the BC₁ population, in which the major one, designated as qHSR1, was mapped on bin 2.09. The anchored ESTs, IDPs, RGAs, BAC and BAC-end sequences in bin 2.09 were exploited to develop markers to saturate the qHSR1 region. The recombinants in the qHSR1 region were obtained by screening the BC₂ population and then backcrossed again to ‘Huangzao4’ to produce 59 BC_2:3 families or selfed to generate nine BC₂F₂ families. Individuals from each BC_2:3 or BC₂F₂ family were evaluated for their resistances to head smut and genotypes at qHSR1. Analysis of genotypes between the resistant and susceptible groups within the same family allows deduction of phenotype of its parental BC₂ recombinant. Based on the 68 BC₂ recombinants, the major resistance QTL, qHSR1, was delimited into an interval of ~2 Mb, flanked by the newly developed markers SSR148152 and STS661. A large-scale survey of BC_2:3 and BC₂F₂ progeny indicated that qHSR1 could exert its genetic effect by reducing the disease incidence by ~25%. Yongsheng Chen, Qing Chao and Guoqing Tan contributed equally to this work.     

Marker-assisted development and evaluation of near-isogenic lines for scab resistance QTLs of wheat

Fusarium head blight or scab resistance in wheat is a complex quantitative trait affected greatly by environments. Therefore, the quantitative trait loci (QTL) for scab resistance found in mapping projects require validation to be effectively utilized in breeding programs. In this study, by employing both forward and background selections with the help of molecular markers, near-isogenic lines (NILs) for scab resistance QTLs Qfh.nau-2B, Qfhs.nau-3B, Qfhi.nau-4B and Qfhi.nau-5A, three of which originating in scab resistance germplasm Wangshuibai, were developed with the elite line Miangyang 99-323 as the recurrent parent. During the process of backcross, selection was based solely on marker genotypes of the target regions, and on recipient genome recovery rate in BC₂F₁ and BC₃F₁. All the identified BC₃F₁ plants with the target QTL regions have more than 94% recipient genome composition (RGC), and out of four to five of them a plant with over 97% RGC were obtained in each backcross combination. Compared with Mianyang 99-323, the Qfhs.nau-3B NIL showed much better resistance to disease spread within spikes, the Qfhi.nau-4B and Qfhi.nau-5A NILs showed much better resistance to initial infection, and the Qfh.nau-2B NIL showed improvement in both types of resistance. These results were consistent with findings in the previous QTL mapping studies. Morphologically and agronomically these NILs were similar to Mianyang 99-323 except that Qfhi.nau-4B NIL was taller and had a longer spike, and Qfhi.nau-5A NIL had narrower leaves. These results demonstrated the feasibility of marker-assisted utilization of scab resistance QTLs.