Molecular mapping of QTL for southwestern corn borer resistance, plant height and flowering in tropical maize

Development of multiple insect resistance in tropical maize represents a major effort of the maize breeding programme at CIMMYT. Resistance to the southwestern corn borer (SWCB) is polygenically controlled with primarily additive gene action. Our main objective was to identify quantitative trait loci (QTL) involved in resistance to SWCB. Other objectives were to detect QTL in the same population for plant height, female flowering, and the anthesis-silking interval (ASI). A population of 472 F₂ individuals derived from a cross between the susceptible line Ki3 and the resistant inbred CML139, was restriction fragment length polymorphism (RFLP) genotyped using 110 maize probes. F₃ families were rated for leaf-feeding damage after artificial infestation at one location in three consecutive years. Height and flowering were measured in protected trials in two locations. QTL analyses were conducted using joint composite interval mapping. Seven QTL on chromosomes 3, 5, 6, 8, and 9 explained 30% of the phenotypic variance (σ²_p) for SWCB damage. Most QTL alleles conferring resistance were contributed from CML139. QTL showed dominance, partial dominance and additive gene action. Eleven QTL dispersed across the genome were determined to affect plant height and explained 43% of σ²_p. Four of these were in close proximity to loci with qualitative effects on plant height. Thirteen QTL (50% of sigma;²_p) were identified for days to female flowering and nine (30% of σ²_p) for ASI. Our results, along with those from other mapping studies at CIMMYT, are allowing us to formulate marker-assisted selection schemes to complement the breeding efforts for such complex traits as borer resistance.     

Molecular mapping and gene action of Scm1 and Scm2, two major QTL contributing to SCMV resistance in maize

Sugarcane mosaic virus (SCMV) is one of the most important virus diseases of maize in Europe. In this study, the gene action at two major quantitative trait loci (QTL) affecting resistance to SCMV in maize was mapped and characterized. A total of 121 F₃ lines from cross F7 (susceptible) × FAP1360A (resistant) were evaluated for SCMV resistance in replicated field trials across two environments under artificial inoculation at seven scoring dates. The genotypic variance was always highly significant and heritability increased up to 0.92 for later scoring dates. The method of composite interval mapping was employed for QTL mapping using four simple sequence repeat (SSR) markers flanking two regions identified in a previous study with cross D145 × D32. The presence of two QTL for SCMV resistance, one on chromosome 6 (Scml region) and one on chromosome 2 (Scm2 region), was confirmed. These two QTL together explained between 15% (first score) and 62% (final score) of the phenotypic variance at various stages of plant development. Gene action was additive for the Scm1 region but completely dominant for the Scm2 region. Comparison of results of this study with those obtained for cross D145 × D32 suggested that the resistance alleles in the two populations are identical for the Scm1 region but different for the Scm2 region.     

Oligogenic control of resistance to soil‐borne viruses SBCMV and WSSMV in rye (Secale cereale L.)

Rye production in European growing areas is constrained by the soilborne cereal mosaic virus (SBCMV) and the wheat spindle streak mosaic virus (WSSMV). To date, no European rye cultivars are known to exhibit resistance against these viruses. In this study, we pursued a quantitative trait locus (QTL) mapping strategy to identify genomic regions for resistance to SBCMV and WSSMV in rye. Three populations, each comprising 100 lines segregating for resistance to SBCMV and/or WSSMV, were evaluated for disease response at two years in three locations in Germany where soils are naturally infested with SBCMV and WSSMV. In the combined analysis across environments, one QTL for SBCMV resistance on chromosome 5R explained 31.9% of the phenotypic variation in one of the populations. For WSSMV resistance, one QTL explaining up to 64.0% of the phenotypic variation was detected on chromosome 7R in each of the three populations. On the Triticeae homoeologous group 5, we found evidence for synteny of the major QTL for SBCMV resistance between the wheat and rye genomes.     

Inheritance of Striga hermonthica adaptive traits in an early‐maturing white maize inbred line containing resistance genes from Zea diploperennis

Striga hermonthica can cause as high as 100% yield loss in maize depending on soil fertility level, type of genotype, severity of infestation and climatic conditions. Understanding the mode of inheritance of Striga resistance in maize is crucial for introgression of resistance genes into tropical germplasm and deployment of resistant varieties. This study examined the mode of inheritance of resistance to Striga in early‐maturing inbred line, TZdEI 352 containing resistance genes from Zea diploperennis. Six generations, P₁, P₂, F₁, F₂, BC₁P₁ and BC₁P₂ derived from a cross between resistant line, TZdEI 352 and susceptible line, TZdEI 425 were screened under artificial Striga infestation at Mokwa and Abuja, Nigeria, 2015. Additive‐dominance model was adequate in describing observed variations in the number of emerged Striga plants among the population; hence, digenic epistatic model was adopted for Striga damage. Dominance effects were higher than the additive effects for the number of emerged Striga plants at both locations signifying that non‐additive gene action conditioned inheritance of Striga resistance. Inbred TZdEI 352 could serve as invaluable parent for hybrid development in Striga endemic agro‐ecologies of sub‐Saharan Africa.     

Molecular mapping of quantitative trait loci for grain moisture at harvest in maize

In maize, high grain moisture (GM) at harvest causes problems in harvesting, threshing, artificial drying, storage, transportation and processing. Understanding the genetic basis of GM will be useful for breeding low‐GM varieties. A quantitative genetics approach was used to identify quantitative trait loci (QTL) related to GM at harvest in field‐grown maize. The GM of a double haploid population consisting of 240 lines derived from Xianyu335 was evaluated in three planting seasons and a high‐density genetic linkage map covering 1546.4 cM was constructed. The broad‐sense heritability of GM at harvest was 71.0%. Using composite interval mapping, six QTL for GM at harvest were identified on five chromosomes (Chr). Two QTL located on Chr1, qgm1‐1 and qgm1‐2, explained 5.0% and 10.8% of the phenotypic variation in GM at harvest, respectively. The QTL qgm2, qgm3, qgm4 and qgm5 accounted for 3.3%, 8.3%, 5.4% and 11.0% of the mean phenotypic variation, respectively. Because of their consistent detection over multiple planting seasons, the detected QTL appear to be robust and reliable for the breeding of low‐GM varieties.     

Genes for resistance to northern corn leaf blight in diverse maize populations

Turcicum or northern corn leaf blight (NCLB) incited by the ascomycete Setosphaeria turcica, anamorph Exserohilum turcicum, is a ubiquitous foliar disease of maize. Diverse sources of qualitative and quantitative resistance are available but qualitative resistances (Ht genes) are often unstable. In the tropics especially, they are either overcome by new virulent races or they suffer from climatically sensitive expression. Quantitative resistance is expressed independently of the physical environment and has never succumbed to S. turcica pathotypes in the field. This review emphasizes the identification and mapping of genes related to quantitative NCLB resistance. We deal with the consistency of the genomic positions of quantitative trait loci (QTL) controlling resistance across different maize populations, and with the clustering of genes for resistance to S. turcica and other fungal pathogens or insect pests in the maize genome. Implications from these findings for further genomic research and resistance breeding are drawn. Incubation period (IP) and area under the disease progress curve (AUDPC), based on multiple disease ratings, are important component traits of quantitative NCLB resistance. They are generally tightly correlated (r_p? 0.8) and highly heritable (h²? 0.75). QTL for resistance to NCLB (IP and AUDPC) were identified and characterized in three mapping populations (A, B, C). Population A, a set of 121‐150 F₃ families of the cross B52×mo17, represented US Corn Belt germplasm with a moderate level of resistance. It was field‐tested in Iowa, USA, and Kenya, and genotyped at 112 restriction fragment length polymorphism (RFLP) loci. Population B consisted of 194‐256 F₃ families of the cross Lo951×CML202, the first parent being a Corn‐Belt‐derived European inbred line and the second parent being a highly resistant tropical African inbred line. The population was also tested in Kenya and genotyped with 110 RFLP markers. Population C was derived from a cross between two early‐maturing European inbred lines, D32 and D145, both having a moderate level of resistance. A total of 220 F₃ families were tested in Switzerland and characterized with 87 RFLP and seven SSR markers. In each of the three studies, 12‐13 QTL were detected by composite interval mapping at a signifcance threshold of LOD=2.5. The phenotypic and the genotypic variance were explained to an extent of 50‐70% and 60‐80%, respectively. Gene action was additive to partly dominant, as in previous generation means and combining ability analyses with other genetic material. In each population, gene effects of the QTL were of similar magnitude and no putative major genes were discovered. QTL for AUDPC were located on chromosomes 1 to 9. All three populations carried QTL in identical genomic regions on chromosomes 3 (bin 3.06/07), 5 (bin 3.06/07) and 8 (bin 8.05/06). The major genes Ht2 and Htn1 were also mapped to bins 8.05 and 8.06, suggesting the presence of a cluster of closely linked major and minor genes. The chromosomal bins 3.05, 5.04 and 8.05, or adjacent intervals, were further associated with QTL and major genes for resistance to eight other fungal diseases and insect pests of maize. Bins 1.05/07 and 9.05 were found to carry population‐specifc genes for resistance to S. turcica and other organisms. Several disease lesion mimic mutations, resistance gene analogues and genes encoding pathogenesis‐related proteins were mapped to regions harbouring NCLB resistance QTL.     

Prediction of deoxynivalenol and zearalenone concentrations in Fusarium graminearum inoculated backcross populations of maize by symptom rating and near‐infrared spectroscopy

Gibberella ear rot (GER) caused by Fusarium graminearum is a destructive disease in maize of temperate regions resulting in yield reduction and contamination by the mycotoxins deoxynivalenol (DON) and zearalenone (ZON). We wanted to analyse whether prediction of DON and ZON concentrations is feasible either by GER severity ratings or by near‐infrared spectroscopy (NIRS). We analysed 80 and 102 lines developed by backcrossing doubled‐haploid lines from segregating populations to the resistant and susceptible parent, respectively, by artificial infection at three locations in Germany and France. Both backcross (BC) populations differed substantially in their means for all traits with significant (P < 0.01) genotypic variances. DON and ZON concentrations measured by immunotests were significantly (P < 0.01) correlated with each other and with GER severity within each BC population (0.6 ≤ r ≤ 0.9, P < 0.01). DON concentration measured by immunotest and NIRS significantly correlated (r ≈ 0.9, P < 0.01). In conclusion, DON and ZON concentrations could be reliably predicted by GER severity. Additional NIRS analysis of DON concentration might be useful for the positively selected fraction.     

Molecular mapping of a major QTL conferring resistance to SCMV based on immortal RIL population in maize

Sugarcane mosaic virus (SCMV) is one of devastating pathogens in maize (Zea mays L.), and causes serious yield loss in susceptible cultivars. An effective solution to control the virus is utilizing resistant genes to improve the resistance of susceptible materials, whereas the basic work is to analyze the genetic basis of resistance. In this study, maize inbred lines Huangzao4 (resistant) and Mo17 (susceptible) were used to establish an F₉ immortal recombinant inbred line (RIL) population containing 239 RILs. Based on this segregation population, a genetic map was constructed with 100 simple sequence repeat (SSR) markers selected from 370 markers, and it covers 1421.5 cM of genetic distance on ten chromosomes, with an average interval length of 14.2 cM. Analysis of the genetic map and resistance by mapping software indicated that a major quantitative trait locus (QTL) was between bin6.00 and bin6.01 on chromosome 6, linked with marker Bnlg1600 (0.1 cM of interval). This QTL could account for 50.0% of phenotypic variation, and could decrease 27.9% of disease index.     

Development and study of a maize cultivar rich in anthocyanins: coloured polenta,a new functional food

Among the phytonutrients, anthocyanins have been extensively studied because of their antioxidant power, the characteristic supposedly responsible for their capacity for chronic disease prevention. Anthocyanins can also be synthesized in maize even though in Europe the colourless varieties have always been preferred. The aim of this study was to develop and characterize a new polenta variety of maize rich in anthocyanins, bred by a recurrent selection scheme, to increase the antioxidant power of this food. The recurrent selection was based on the anthocyanin content and other specific traits of the kernel. The coloured polenta obtained was analysed by TLC (Thin Layer Chromatography) analysis and DPPH (2,2‐diphenyl‐1‐picrylhydrazyl) radical scavenging ability, before and after cooking. The results obtained showed that even though cooking reduced the anthocyanin content by about 22%, the remaining anthocyanins exhibited twofolds higher antioxidant capacity, expressed as ARP (antiradical power) using acetone/water extraction buffer in DPPH assay, compared to the colourless control. Furthermore, our data showed that the anthocyanin content did not alter the taste of the coloured polenta.     

QTL mapping of net blotch resistance genes in a doubled-haploid population of six-rowed barley

Net blotch, caused by Pyrenophora teres f. teres, is a damaging foliar disease of barley worldwide. It is important to identify resistance germplasm and study their genetics. 'Chevron', a six-rowed barley used as a parent for the production of a doubled haploid (DH) population for mapping of Fusarium head blight (FHB) resistance, was also found to be resistant to net blotch. To map the resistance genes, the population was evaluated for resistance at the seedling stage in a greenhouse. The resistance data showed a two-peak distribution. Through linkage mapping, one resistance gene, tentatively called Rpt, was located on chromosome 6HS flanked by Xksua3b-Xwg719d, which was also detected by QTL mapping. This QTL explained 64% of the phenotypic variance for the resistance in this DH population. In addition, a minor QTL was found on chromosome 2HS defined by Xcdo786-Xabc156a. 'Chevron' and 'Stander' contributed the resistant alleles of Rpt and the 2HS QTL, respectively. Both QTLs together explained nearly 70% of the phenotypic variance. The markers for these QTLs are useful for marker-assisted selection of net blotch resistance in barley breeding.     

Identification of QTL controlling high levels of partial resistance to Fusarium solani f. sp. pisi in pea

Fusarium root rot is a common biotic restraint on pea yields, and genetic resistance is the most feasible method for improving pea production. This study was conducted to discover quantitative trait loci (QTL) controlling genetic partial resistance to Fusarium root rot caused by Fusarium solani (Mart.) Sacc. f.sp. pisi (F.R. Jones) W.C. Snyder & H.N. Hans (Fsp). A RIL population was screened in a Fusarium root rot field disease nursery for 3 years. Composite interval mapping was employed for QTL detection using the means of disease severity from three growing seasons. Five QTL were identified, including one QTL identified in all three years. The multiyear QTL Fsp‐Ps2.1 contributed to a significant portion of the phenotypic variance (22.1–72.2%), while a second QTL, Fsp‐Ps6.1, contributed 17.3% of the phenotypic variance. The other single growing season QTL are of additional interest as they colocate with previously reported pea–Fusarium root rot resistance QTL. QTL Fsp‐Ps2.1, Fsp‐Ps3.1, Fsp‐4.1 and Fsp‐Ps7.1 are flanked by codominant SSRs and may be useful in marker‐assisted breeding of pea for high levels of partial resistance to Fsp.     

Interaction of common bacterial blight quantitative trait loci in a resistant inter‐cross population of common bean

Common bacterial blight (CBB), caused by Xanthomonas axonopodis pv. phaseoli, is an important disease of common bean (Phaseolus vulgaris L.). Genetic resistance is the most economically efficient, environmentally friendly and socially acceptable approach to control plant diseases including CBB. To examine the main and interaction effects of the previously identified CBB resistance quantitative trait loci (QTL) associated with markers BC420 (B) on Pv06, SAP6 (S) on Pv10 and PVctt001 (P) on Pv04, in presence of the major QTL associated with the marker SU91 (S_u) on Pv08, a resistant F_4:5 recombinant inbred line population of the reciprocal crosses between OAC Rex (bb/ss/PP/S_uS_u) and HR45 (BB/SS/pp/S_uS_u) was evaluated under artificial field inoculation in disease nurseries in 2009 and 2010. While, in presence of the CBB QTL on Pv08, the QTL on Pv06 of HR45 accounted for 37–46% of phenotypic variation in the field, the effect of QTL on Pv04 and Pv10 were not significant under field conditions, even in the absence of the Pv06 QTL. Broad‐sense heritability estimates of CBB resistance and the QTL associated with BC420 were high for CBB severity and the area under the disease progress curve, promoting the continued efforts in pyramiding the QTL on Pv06 and Pv08 in common background, which provide high levels of resistance.     

QTL analysis for cooking traits of super rice with a high‐density SNP genetic map and fine mapping of a novel boiled grain length locus

Hybrid rice has contributed substantially to the improvement of grain production worldwide, yet its poor cooking and tasting characteristics have long been recognized. In this study, 132 recombinant inbred lines derived from LYPJ were used to identify quantitative trait loci (QTLs) for 12 cooking traits with the high‐density SNP linkage map recently developed by our team. We identified 17 QTLs on chromosomes 1, 2, 4, 5, 6, 7, 8, 9 and 11, which accounted for 7.50% to 23.50% of the phenotypic variations. A novel major QTL qBGL7 for boiled grain length was further fine‐mapped to an interval of 440 Kb between the two markers RM21906 and gl3 using a BC₃F₂ population. Two near‐isogenic lines with extreme boiled grain length, GX5‐176 and GX5‐101, could be directly used in improving cooking quality. We also identified a QTL for soaked grain width expansion rate, qSGWE6, in the Wx gene region on chromosome 6. The Wx differential regulation coincided with sequential variation between the two parents. Our work offered a theoretical basis for molecular breeding of high‐quality hybrid rice.     

QTL for maize grain yield identified by QTL mapping in six environments and consensus loci for grain weight detected by meta‐analysis

Grain yield is the most important and complicated trait in maize. In this study, a total of 498 recombinant inbred lines (RIL) derived from a biparental cross of two elite inbred lines, 178 and P53, were grown in six different environments. Quantitative trait locus (QTL) mapping was conducted for three grain yield component traits (100 grain weight, ear weight and kernel weight per plant). Subsequently, meta‐analysis was performed after a comprehensive review of the research on QTL mapping for grain weight (100, 300 and 1000) using BioMercator V4.2. In total, 62 QTLs were identified for 100 grain weight, ear weight and kernel weight per plant in six environments. Forty‐three meta‐QTLs (MQTLs) were detected by meta‐analysis. A total of 13 candidate genes homologous to eight functionally characterized rice genes were found, and four candidate genes were located in the two hot spot regions of MQTL1.5 and MQTL2.3. Our results suggest that the combination of literature collection, meta‐analysis and homologous blast searches can offer abundant information for further fine mapping, marker‐assisted selection (MAS) breeding and map‐based cloning for maize.     

Multiple‐line cross QTL mapping for grain yield and thousand kernel weight in triticale

Grain yield and its component trait thousand kernel weight are important traits in triticale breeding programmes. Here, we used a large mapping population of 647 doubled haploid lines derived from four families to dissect the genetic architecture underlying grain yield and thousand kernel weight by multiple‐line cross QTL mapping. We identified 3 QTL for grain yield and 13 for thousand kernel weight which cross‐validated explained 5.2% and 48.2% of the genotypic variance, respectively. Both traits showed a positive phenotypic correlation, and we found two QTL overlapping between them. Full two‐dimensional epistasis scans revealed epistatic QTL for both traits, suggesting that epistatic interactions contribute to their genetic architecture. Based on QTL identified in our results, we conclude that the potential for marker‐assisted selection is limited for grain yield but more promising for thousand kernel weight.     

Fine mapping of a day‐length‐sensitive dwarf gene in rice

Dwarf mutants are valuable and crucial resources for genetic research and crop breeding programme in rice. In this study, we identified a dwarf mutant derive from tissue culture, which exhibited a delayed heading date and dwarfism under long‐day growth conditions, suggesting the heading date of dwarf mutant was sensitive to day length. Based on 2000 F₂ mutant‐like individuals from the cross of the mutant and a Japonica var. ‘IRAT129’, the dwarf gene was finally narrowed into a 512‐kb region near the centromere on chromosome 9. According to the sequence analysis of a delimited region, 21 genes had base alternations either in promoters (15 SNPs) or in coding regions (6 InDels) among 73 annotated genes, and five genes were confirmed sequence alternations resulting from their expression mainly in the vegetative organs. Given to the RNAi plants of the five genes incapable to mimic dwarf and late heading date phenotype, the candidate gene remains to be identified by other genetic or molecular methods. Therefore, all these results give us informative foundation for the day‐length‐sensitive dwarf gene isolation.     

RNAi‐based Bean golden mosaic virus‐resistant common bean (Embrapa 5.1) shows simple inheritance for both transgene and disease resistance

Bean golden mosaic virus (BGMV) is the causal agent of bean golden mosaic of common beans. A transgenic bean line that has been developed based on RNA interference to silence the BGMV rep gene showed immunity to the virus. Crosses were done between the transgenic line and six bean cultivars followed by four backcrosses to the commercial cultivars ‘Pérola’ and ‘BRS Pontal’. The transgene locus was consistently inherited from the crosses analysed in a Mendelian fashion in the segregating populations. The disease resistance reaction co‐inherited with the transgene. Nevertheless, the expression of disease resistance displayed a dosage effect phenomenon in the F₁ generation. The analysis of the homozygous near‐isogenic lines in field conditions, under high BGMV disease incidence, indicated that the transgenic lines were completely resistant. These results show the strength of the disease resistance obtained, the stability of the trait across generations and its usefulness in the management of a disease for which there is no reported Phaseolus germplasm with immunity.     

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.