Quantitative trait loci for quality and agronomic traits in two advanced backcross populations in oat (Avena sativa L.)

Using the advanced backcross quantitative trait loci (AB‐QTL) strategy, we successfully transferred and mapped valuable allelic variants from the high β‐glucan (BG) accession IAH611 (PI 502955), into the genome of cultivar ‘Iltis’. By backcrossing one BC₁F₁ plant to ‘Iltis’, we developed two BC₂F_2‐6 populations A and B, comprising 98 and 72 F₂‐individuals, respectively. Genotyping of BC₂F₂ individuals with predominantly AFLP markers resulted in 12 linkage groups with a map size of 455.4 cM for Population A and 11 linkage groups with a map size of 313.5 cM for Population B. Both populations were grown at three sites in Germany over a three‐year period. Individuals were then phenotyped for 13 traits including grain yield (YD) and β‐glucan content (BG). QTL analysis via stepwise regression detected a total of 33 QTLs, most of which were clustered in three linkage groups. Two dense linkage groups A1 and B13 were found to be putatively homologous to groups KO_6 and KO_11 of the ‘Kanota’/‘Ogle’ map, respectively.     

Mapping of quantitative trait loci for resistance to race 1 of Pyrenophora tritici‐repentis in synthetic hexaploid wheat

Tan spot, caused by a necrotrophic fungus Pyrenophora tritici‐repentis (Ptr), has become an important foliar disease of wheat worldwide. Effective control of tan spot can be achieved by deployment of resistant wheat cultivars. An F_2:3 population derived from a cross between synthetic hexaploid wheat (SHW), TA4161‐L1 (moderately resistant) and susceptible winter wheat cultivar, ‘TAM105’ was evaluated with race 1 of Ptr under controlled conditions. The population was genotyped using Diversity Arrays Technology (DArT). Presence of transgressive segregants indicated contribution of positive alleles from both parents. Two major QTLs were located on the short arm of chromosomes 1A and 6A and designated as QTs.ksu‐1A and QTs.ksu‐6A, respectively. Two additional QTLs were identified on chromosome 7A. Resistant alleles of all the QTLs were contributed by TA4161‐L1. Novel QTLs on 6A and 7A can be a valuable addition to known resistance genes and utilized in breeding programmes to produce highly resistant cultivars.     

雪茄烟品种Beinhart1000-1赤星病抗性基因的QTL定位

由链格孢菌(Alternariaalternata)引起的赤星病是最具破坏性的烟草叶斑病害之一,在中国严重地影响烟草(Nicotiana tabacum L.)的产量和质量。选育抗烟草赤星病的优良品种虽是预防该病最经济、有效的途径,但因其抗性受数量性状基因控制而很难通过常规育种手段实现。为了便于开展烟草抗赤星病分子标记辅助选择育种,本研究利用抗赤星病雪茄烟品种Beinhart1000-1和感病烤烟品种红花大金元经杂交、自交产生的362个F_2单株构建了一张包含670个SSR标记的烟草遗传连锁图谱,并结合组培快繁形成的F_2株系的田间赤星病病情指数(DI),在全基因组范围内检测获得2个与烟草赤星病抗性相关的QTL,分别位于第20和23连锁群上的SSR标记TMs05179和TMs04022,以及TM61049和TM62212之间。这2个QTL等位基因均来自抗病亲本Beinhart1000-1,它们一起解释了两亲本间81%的病情指数(DI)差异及64%的加性效应。为下一步开展烟草抗赤星病的分子标记辅助育种奠定了基础。     

Use of non‐adapted quantitative trait loci for increasing Fusarium head blight resistance for breeding semi‐dwarf wheat

Semi‐dwarf wheat is an important prerequisite for releasing a successful commercial cultivar in high‐yielding environments. In Northern Europe, this aim is achieved by using one of the dwarfing genes Rht‐B1 (formerly known as Rht‐1) or Rht‐D1 (Rht‐2). Both genes, however, result in a higher susceptibility to Fusarium head blight (FHB). We analysed the possibility to use the two non‐adapted FHB resistance quantitative trait loci Fhb1 and Fhb5 (syn. QFhs.ifa‐5A) to counterbalance the negative effect of the dwarfing allele Rht‐D1b in a winter wheat population of 585 doubled‐haploid (DH) lines segregating for the three loci. All lines were inoculated with Fusarium culmorum at four locations and analysed for FHB severity, plant height, and heading date. The DH population showed a significant (p < 0.001) genotypic variation for FHB severity ranging from 3.6% to 65.9% with a very high entry‐mean heritability of 0.95. The dwarfing allele Rht‐D1b reduced plant height by 24 cm, but nearly doubled the FHB susceptibility (24.74% vs. 12.74%). The resistance alleles of Fhb1 and Fhb5 reduced FHB susceptibility by 6.5 and 11.3 percentage points, respectively. Taken all three loci together, Fhb5 alone was already able to reduce FHB susceptibility to the same extent as Rht‐D1b increased it. This opens new avenues for selecting semi‐dwarf wheat by marker‐assisted introgression of Fhb5 without the enhancement of FHB susceptibility.     

An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.     

A fine‐scale genetic linkage map reveals genomic regions associated with economic traits in walnut (Juglans regia)

A genetic linkage map of walnut containing 2,220 single nucleotide polymorphisms (SNPs) in 16 linkage groups (LGs) was constructed using an F₁ mapping population from a cross between “Chandler” and “Idaho,” two contrasting heterozygous parents. Five quantitative yield traits, lateral fruitfulness, harvest date and three nut traits (shell thickness, nut weight and kernel fill) were then mapped on to linkage groups. A significant quantitative trait locus (QTL) in LG 11 with negative additive effects suggested heterozygote superiority in the expression of lateral bearing. A set of three QTLs explaining ~10% of the variation in harvest date was located in LG 1. Shell thickness, nut weight and kernel fill were under the control of two to three linked pleiotropic QTLs in LG 1 segregating from “Idaho.” The marginal positive additive effects of QTLs for harvest date, shell thickness and nut weight and small negative additive effects for kernel fill suggested that the QTLs had a marginal effect on the expression of these traits.     

Molecular mapping of quantitative trait loci for ascochyta blight and botrytis grey mould resistance in an inter-specific cross in chickpea (Cicer arietinum L.) using genotyping by sequencing

Ascochyta blight (AB) and botrytis grey mould (BGM) are the most devastating fungal diseases of chickpea worldwide. The wild relative of chickpea, C. reticulatum acc. ILWC 292 was found resistant to BGM whereas, GPF2 (Cicer arietinum L.) is resistant to AB. A total of 187 F₈ Recombinant Inbred Lines (RILs) developed from an inter-specific cross of GPF2 × C. reticulatum acc. ILWC 292 were used to identify quantitative trait loci (QTLs) responsible for resistance to AB and BGM. RILs along with parents were evaluated under artificial epiphytotic field/laboratory conditions for two years. Highly significant differences (P < 0.001) were observed for reaction to both pathogens in both years. Parents and RILs were genotyped-by-sequencing to identify genome wide single nucleotide polymorphism (SNPs). A total of 1365 filtered and parental polymorphic SNPs were used for linkage map construction, of which, 673 SNPs were arranged on eight linkage groups. Composite interval mapping revealed three QTLs for AB and four QTLs for BGM resistance. Out of which, two QTLs for AB and three QTLs for BGM were consistent in both years. These QTLs can be targeted for further fine mapping for deployment of resistance to AB and BGM in elite chickpea cultivars using marker-assisted-selection.     

Construction of a genetic linkage map and QTL analysis of fiber-related traits in upland cotton (Gossypium hirsutum L.)

A genetic linkage map with 70 loci (55 SSR, 12 AFLP and 3 morphological loci) was constructed using 117 F₂ plants obtained from a cross between two upland cotton cultivars Yumian 1 and T586, which have relatively high levels of DNA marker polymorphism and differ remarkably in fiber-related traits. The linkage map comprised of 20 linkage groups, covering 525 cM with an average distance of 7.5 cM between two markers, or approximately 11.8% of the recombination length of the cotton genome. The present genetic linkage map was used to identify and map the quantitative trait loci (QTLs) affecting lint percentage and fiber quality traits in 117 F_2:3 family lines. Sixteen QTLs for lint percentage and fiber quality traits were identified in six linkage groups by multiple interval mapping: four QTLs for lint percentage, two QTLs for fiber 2.5% span length, three QTLs for fiber length uniformity, three QTLs for fiber strength, two QTLs for fiber elongation and two QTLs for micronaire reading. The QTL controlling fiber-related traits were mainly additive, and meanwhile including dominant and overdominant. Several QTLs affecting different fiber-related traits were detected within the same chromosome region, suggesting that genes controlling fiber traits may be linked or the result of pleiotropy.     

Identification and application of major quantitative trait loci for panicle length in rice (Oryza sativa) through single‐segment substitution lines

Panicle length (PL), an important yield‐related trait, strongly affects yield components, such as grain number, grain density and rice quality. More than 200 panicle length quantitative trait loci (PL QTLs) are identified, but only a small number are applied in rice breeding. In this study, we performed QTL analysis for PL using 42 single‐segment substitution lines (SSSLs) derived from nine donors in the genetic background of HJX74. Fourteen QTLs and five heterosis QTLs (HQTLs) for PL were recognised. Three QTLs and four HQTLs acted positively, and the other eleven QTLs and one HQTL acted negatively. By scanning the single heterozygous background region of the F₂ population with large‐genetic‐effect SSSLs, we mapped PL loci qPL6‐2 and qPL7‐1 to different locations on chromosomes 6 and 7, respectively, in three consecutive years of independent trials. The genetic effects of these QTLs were further assessed. qPL6‐2 demonstrated the most positive additive effect (QTL), whereas qPL7‐1 achieved the most positive dominant effect (HQTL) for PL. These results indicated that the pyramiding of PL QTLs might increase grain yield and facilitate the application of the beneficial allele in hybrid rice breeding.     

Growth response of 98 barley (Hordeum vulgare L.) genotypes to elevated CO2 and identification of related quantitative trait loci using genome‐wide association studies

Elevated CO₂ (eCO₂) concentrations can stimulate crop growth, but little is known about intraspecific variability in the response to eCO₂ and the underlying genetics in cereals. Field experiments over two years with 98 barley genotypes were conducted in open‐top chambers (OTCs) under ambient CO₂ (400 ppm) and eCO₂ (700 ppm) concentrations. At crop maturity, different fractions of aboveground biomass (AGB) were measured, and genome‐wide association studies (GWASs) were conducted to identify quantitative trait loci (QTL). Averaged across all genotypes, eCO₂ significantly enhanced AGB by 15%, while the increase in culm and ear biomass alone was not significant. The AGB response to eCO₂ of the individual genotypes ranged from c. ?36% to +95% compared with ambient CO₂ (aCO₂), showing a large variability of growth responses. In GWAS, 51 associations between SNP markers and the relative changes (eCO₂/aCO₂) in biomass were detected on different chromosomes. Loci potentially involved in biomass alterations under eCO₂ were identified. The wide range of variability in responses might be exploited by marker‐based breeding for climate‐resilient barley.