In vitro screening and QTL analysis for drought tolerance in diploid potato

Drought stress is a major abiotic constraint limiting crop production worldwide. Screening for drought tolerance and the traits that enhance drought tolerance is not straightforward in large mapping populations. In this study, we investigated the possibility of screening a mapping population in vitro for PEG-induced water deficit stress and recovery potential. We have measured several shoot and root growth parameters or traits in the C × E diploid potato mapping population. Significant variation was observed for genotype-specific responses to water deficit and recovery potential. Genetic variation and heritability estimates were high to very high for the measured traits depending on growth conditions. In order to identify potato QTLs for drought tolerance and recovery potential an SNP marker-rich integrated linkage map was used. A total of 23 QTLs were detected under control, stress and recovery treatments explaining 10.3–22.4% of the variance for each phenotypic trait. Among these, 10 QTLs were located on chromosome 2. Three QTLs involved in the important trait root to shoot ratio were identified on linkage groups 2, 3 and 8. These loci explained together 41.1% of the variance for this trait, and may be breeding targets for stress tolerance and yield in the field as well. The SNP markers derived from EST sequences underlying these QTLs led to the identification of putative candidate genes for further study in potato. This study constitutes the first knowledge of in vitro screening of a mapping population for drought tolerance in potato.     

Crop breeding for salt tolerance in the era of molecular markers and marker‐assisted selection

Crop salt tolerance (ST) is a complex trait affected by numerous genetic and non‐genetic factors, and its improvement via conventional breeding has been slow. Recent advancements in biotechnology have led to the development of more efficient selection tools to substitute phenotype‐based selection systems. Molecular markers associated with genes or quantitative trait loci (QTLs) affecting important traits are identified, which could be used as indirect selection criteria to improve breeding efficiency via marker‐assisted selection (MAS). While the use of MAS for manipulating simple traits has been streamlined in many plant breeding programmes, MAS for improving complex traits seems to be at infancy stage. Numerous QTLs have been reported for ST in different crop species; however, few commercial cultivars or breeding lines with improved ST have been developed via MAS. We review genes and QTLs identified with positive effects on ST in different plant species and discuss the prospects for developing crop ST via MAS. With the current advances in marker technology and a better handling of genotype by environment interaction effects, the utility of MAS for breeding for ST will gain momentum.     

QTL mapping for six ear leaf architecture traits under water‐stressed and well‐watered conditions in maize (Zea mays L.)

Morphological traits for ear leaf are determinant traits influencing plant architecture and drought tolerance in maize. However, the genetic controls of ear leaf architecture traits remain poorly understood under drought stress. Here, we identified 100 quantitative trait loci (QTLs) for leaf angle, leaf orientation value, leaf length, leaf width, leaf size and leaf shape value of ear leaf across four populations under drought‐stressed and unstressed conditions, which explained 0.71%–20.62% of phenotypic variation in single watering condition. Forty‐five of the 100 QTLs were identified under water‐stressed conditions, and 29 stable QTLs (sQTLs) were identified under water‐stressed conditions, which could be useful for the genetic improvement of maize drought tolerance via QTL pyramiding. We further integrated 27 independent QTL studies in a meta‐analysis to identify 21 meta‐QTLs (mQTLs). Then, 24 candidate genes controlling leaf architecture traits coincided with 20 corresponding mQTLs. Thus, new/valuable information on quantitative traits has shed some light on the molecular mechanisms responsible for leaf architecture traits affected by watering conditions. Furthermore, alleles for leaf architecture traits provide useful targets for marker‐assisted selection to generate high‐yielding maize varieties.     

Detection of epistatic and environmental interaction QTLs for leaf orientation‐related traits in maize

Leaf architecture traits in maize are quantitative and have been studied by quantitative trait loci (QTLs) mapping. However, additional QTLs for these traits require mapping and the interactions between mapped QTLs require studying because of the complicated genetic nature of these traits. To detect common QTLs and to find new ones, we investigated the maize traits of leaf angle, leaf flagging‐point length, leaf length and leaf orientation value using a set of recombinant inbred line populations and single nucleotide polymorphism markers. In total, 19 QTLs contributed 4.13–13.52% of the phenotypic effects to the corresponding traits that were mapped, and their candidate genes are provided. Common and major QTLs have also been detected. All of the QTLs showed significant additive effects and non‐significant additive × environment effects in combined environments. The majority showed additive × additive epistasis effects and non‐significant QTL × environment effects under single environments. Common and major QTLs provided information for fine mapping and gene cloning, and SNP markers can be used for marker‐assisted selection breeding.     

Identification of near-isogenic lines: an innovative approach,validated for root and shoot morphological characters in a mapping population of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Near-isogenic lines (NILs) constitute valuable tools in genetic investigations and plant breeding programs. Conventional methods for developing these are time consuming and tedious. An innovative method for identifying NILs is proposed and validated. The method involves computation of simple correlation coefficients of all possible pairs of genotypes within a mapping population using molecular marker data, and phenotypic characterization of those pairs with very high positive correlation. The pairs having both genomic and phenotypic similarity except for a single trait are considered as NILs. This strategy was tested with a doubled haploid mapping population involving CT9993 and IR62266. This population was saturated with 315 markers and comprised 154 lines. The pairs showing very high correlation coefficients (0.70–0.97) and differing for less than 10% of the markers were considered as Genotypically Closely Related Pairs (GCRPs). Graphical genotyping was employed to visualize the genome of the closely related lines. A total of 39 such pairs were subjected to rigorous evaluation for root and shoot morphological traits in two contrasting moisture regimes. Four GCRPs under well-watered condition and ten GCRPs under low moisture stress condition are statistically significant for a single phenotypic trait and are considered as NILs for their respective traits and would be the valuable materials for genetic studies. Mapped QTLs and candidate genes were employed to explain the probable cause of phenotypic difference in NILs.     

Functional mechanisms of drought tolerance in maize through phenotyping and genotyping under well watered and water stressed conditions

Developing tolerant genotypes is crucial for stabilizing maize productivity under drought stress conditions as it is one of the most important abiotic stresses affecting crop yields. Twenty seven genotypes of maize (Zea mays L.) were evaluated for drought tolerance for three seasons under well watered and water stressed conditions to identify interactions amongst various tolerance traits and grain yield as well as their association with SSR markers. The study revealed considerable genetic diversity and significant variations for genotypes, environment and genotype × environment interactions for all the traits. The ranking of genotypes based on drought susceptibility index for morpho-physiological traits was similar to that based on grain yield and principal component analysis. Analysis of trait – trait and trait – yield associations indicated significant positive correlations amongst the water relations traits of relative water content (RWC), leaf water potential and osmotic potential as well as of RWC with grain yield under water stressed condition. Molecular analysis using 40 SSRs revealed 32 as polymorphic and 62 unique alleles were detected across 27 genotypes. Cluster analysis resulted in categorization of the genotypes into five distinct groups which was similar to that using principal component analysis. Based on overall performance across seasons tolerant and susceptible genotypes were identified for eventual utilization in breeding programs as well as for QTL identification. The marker-trait association analysis revealed significant associations between few SSR markers with water relations as well as yield contributing traits under water stressed conditions. These associations highlight the importance of functional mechanisms of intrinsic tolerance and cumulative traits for drought tolerance in maize.     

Mapping QTLs in breeding for drought tolerance in maize (Zea mays L.)

Summary Grain yield in the maize (Zea mays L) plant is sensitive to drought in the period three weeks either side of flowering. Maize is well-adapted to the use of restriction fragment length polymorphisms (RFLPs) to identify a tight linkage between gene(s) controlling the quantitative trait and a molecular marker. We have determined the chromosomal locations of quantitative trait loci (QTLs) affecting grain yield under drought, anthesis-silking interval, and number of ears per plant. The F₃ families derived from the cross SD34(tolerant) × SD35 (intolerant) were evaluated for these traits in a two replicated experiment. RFLP analysis of the maize genome included non-radioactive DNA-DNA hybridization detection using chemiluminescence. To identify QTLs underlying tolerance to drought, the mean phenotypic performances of F₃ families were compared based on genotypic classification at each of 70 RFLP marker loci. The genetic linkage map assembled from these markers was in good agreement with previously published maps. The phenotypic correlations between yield and other traits were highly significant. In the combined analyses, genomic regions significantly affecting tolerance to drought were found on chromosomes 1,3,5,6, and 8. For yield, a total of 50% of the phenotypic variance could be explained by five putative QTLs. Different types of gene action were found for the putative QTLs for the three traits.     

QTL analysis of variation for vigour in rose

The improvement of energy efficiency in the greenhouse production of cut rose and pot rose can be achieved through the use of rose cultivars having vigorous growth. A better understanding of the inheritance of vigour and its related traits will assist the breeding activities. Quantitative trait locus (QTL) analyses were performed with the help of an integrated linkage map of a diploid rose population originating from a cross between Rosa multiflora-derived genotypes. The underlying datasets for ten vigour-related traits were collected in an evaluation study of this population in two greenhouse experiments with suboptimal temperatures for growth. We identified ten chromosomal regions, scattered over the seven linkage groups, containing QTLs for these traits. Considering each trait separately, we detected a total of 42 QTLs. Among these QTLs, 24 were found in both of the experiments, eight and ten were specific to either of the two experiments. The number of QTLs for individual traits varied from three to five with a respective contribution to the phenotypic variation from 12 to 35%. QTLs for highly correlated traits frequently co-localized, indicating a common genetic basis. Clustering of QTLs for different traits was noted in some chromosome regions, for instance, one on chromosome 2 included major QTLs for eight of ten traits under study, suggesting co-localization of several separate genes or/and the occurrence of various genes having pleiotropic effects. The discovery of markers associated to QTL regions is in roses the first step towards marker-assisted selection for vigour improvement enabling the transfer of useful QTL-alleles of R. multiflora to pot and cut roses.     

Identification of candidate genes associated with resistance to bruchid (Callosobruchus maculatus) in cowpea

Cowpea is an important legume crop widely grown in sub‐Saharan Africa for food and feed. However, it is largely challenged by bruchid, a serious storage pest resulting in losses in quantity and quality of grains. Therefore, this research was designed to contribute to the breeding of cowpea resistance to bruchid through the identification of candidate genes associated with resistance to bruchid. A total of 217 mini‐core cowpea accessions were genotyped and phenotyped for their reactions to bruchid. To determine the genomic regions linked with bruchid resistance, 41,948 polymorphic SNP markers were used. Genome‐wide association study identified 11 SNPs linked to the average number of eggs, holes, insect emergence and development period and Dobie susceptibility index. Gene search via Phytozome identified six candidate genes (Vigun08g132300, Vigun08g158000, Vigun06g053700, Vigun02g131000, Vigun01g234900 and Vigun01g201900) associated with the resistance traits. These candidate genes could be incorporated into the farmers preferred but susceptible cowpea varieties to bruchid. The SNP markers associated with the resistance traits can be used in marker‐assisted breeding for accurate and rapid screening of cowpea resistant genotypes to bruchid.     

Mapping of quantitative trait loci for floral scent compounds in cowpea (Vigna unguiculata L.)

Floral scent is a very important trait in plant evolution. Currently, little is known about the inheritance of floral scent in cowpea (Vigna unguiculata L.) or changes that might have occurred during its domestication. Therefore, we analysed scent volatiles and molecular markers in a population of 159 F₇ recombinant inbred lines derived from a cross of a domesticated blackeye cowpea cultivar, ‘524B’ and a wild accession ‘219‐01’. Using gas chromatography‐mass spectrometry (GC–MS) 23 volatile compounds were identified that fall into five general functional categories. Twenty‐two of the compounds displayed quantitative variation in the progeny, and a total of 63 QTLs influencing the amounts of these volatiles were mapped onto the cowpea genetic marker map. Although QTLs for volatile compounds putatively involved in cowpea flower scent were found on 9 of the 11 cowpea chromosomes, they were not evenly distributed with QTLs mainly clustered on LGs 1, LGs 2 and LG 4. Our results serve as a starting point for both more detailed analyses of complex scent biosynthetic pathways and the development of markers for marker‐assisted breeding of scented rose varieties.     

Locating QTLs controlling constitutive root traits in the rice population IAC 165 × Co39

Drought is an important constraint to productivity in rainfed rice environments. Improvement in the various components of rice drought tolerance is now possible through the identification and manipulation of DNA markers linked with genes controlling these quantitative traits. A recombinant inbred line population was derived from the cross IAC165 × Co39. A molecular map was built that contained 182 RFLP and microsatellite markers. Segregation distortions were limited to a few chromosomal segments. Constitutive root traits, including maximum root length, root thickness and root dry weight in various layers, were measured on 125 lines in a greenhouse replicated experiment. QTL analysis was performed using composite interval mapping. Between 1and 4 main effect QTLs, which explained individually between 5.5 and 24.8% of the variability, were identified for each trait. The most important genomic regions, which carried QTLs for several traits, were found on chromosomes 1, 4, 9, 11 and 12.The QTL locations were in good agreement with previous studies on these traits, confirming the value of the QTLs in a different genetic background. Epistasis represented a non-negligible component of the observed variability for some of the traits but was not detected for others. These results add to the understanding of the genetic control of root morphology in rice, which is necessary to strengthen marker-aided selection programs to improve varieties for water-limited environments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map

Drought is a major abiotic constraint for rice production worldwide. The quantitative trait loci (QTLs) for drought tolerance traits identified in earlier studies have large confidence intervals due to low density linkage maps. Further, these studies largely focused on the above ground traits. Therefore, this study aims to identify QTLs for root and shoot traits at the vegetative growth stage using a genotyping by sequencing (GBS) based saturated SNP linkage map. A recombinant inbred line (RIL) population from a cross between Cocodrie and N-22 was evaluated for eight morphological traits under drought stress. Drought was imposed to plants grown in 75 cm long plastic pots at the vegetative growth stage. Using a saturated SNP linkage map, 14 additive QTLs were identified for root length, shoot length, fresh root mass, fresh shoot mass, number of tillers, dry root mass, dry shoot mass, and root-shoot ratio. Majority of the drought responsive QTLs were located on chromosome 1. The expression of QTLs varied under stress and irrigated condition. Shoot length QTLs qSL1.38 and qSL1.11 were congruent to dry shoot mass QTL qDSM1.38 and dry root mass QTL qDRM1.11, respectively. Analysis of genes present within QTL confidence intervals revealed many potential candidate genes such as laccase, Calvin cycle protein, serine threonine protein kinase, heat shock protein, and WRKY protein. Another important gene, Brevis radix, present in the root length QTL region, was known to modulate root growth through cell proliferation and elongation. The candidate genes and the QTL information will be helpful for marker-assisted pyramiding to improve drought tolerance in rice.     

Cowpea (Vigna unguiculata): Genetics,genomics and breeding

Cowpea, Vigna unguiculata (L.), is an important grain legume grown in the tropics where it constitutes a valuable source of protein in the diets of millions of people. Some abiotic and biotic stresses adversely affect its productivity. A review of the genetics, genomics and breeding of cowpea is presented in this article. Cowpea breeding programmes have studied intensively qualitative and quantitative genetics of the crop to better enhance its improvement. A number of initiatives including Tropical Legumes projects have contributed to the development of cowpea genomic resources. Recent progress in the development of consensus genetic map containing 37,372 SNPs mapped to 3,280 bins will strengthen cowpea trait discovery pipeline. Several informative markers associated with quantitative trait loci (QTL) related to desirable attributes of cowpea were generated. Cowpea genetic improvement activities aim at the development of drought tolerant, phosphorus use efficient, bacterial blight and virus resistant lines through exploiting available genetic resources as well as deployment of modern breeding tools that will enhance genetic gain when grown by sub‐Saharan Africa farmers.     

A reexamination of molecular markers for use in marker-assisted breeding in tomato

Molecular markers have been used for identification and mapping of genes and QTLs for numerous agriculturally important traits in tomato, including resistance/tolerance to biotic and abiotic stresses and fruit- and flower-related characteristics. However, the extent to which markers have been utilized in tomato breeding programs has not been clearly determined. A review of the literature indicated that the utility of most markers for use in tomato breeding programs have not been verified. Many markers are not validated across tomato genotypes or are not polymorphic within tomato breeding populations. In this study, we examined the utility of available markers for several major disease resistance traits in tomato by testing them in a number of breeding lines and commercial cultivars with known resistance/susceptibility responses. While several markers were validated, others needed PCR optimization for successful amplifications or were not informative in the genotypes used. Specifically, of the 37 markers examined 19 (~51%) were informative, including markers for resistance to Fusarium wilt, late blight, bacterial wilt, tomato mosaic virus, tomato spotted wilt virus, and root knot nematodes. It appears that many of the available markers may need to be further refined or examined for trait association and presence of polymorphism in breeding lines and populations. However, with recent advances in tomato sequencing, it is becoming increasingly possible to develop more informative markers to accelerate the use of MAS in tomato breeding.     

Tolerance to paraquat is correlated with the traits associated with water stress tolerance in segregating F2 populations of barley and wheat

To identify scorable marker traits that can be used in cereal breeding programs for selecting drought tolerant individuals, we investigated the correlation among the drought-associated traits in two F₂ populations derived from the crosses made between drought tolerant and sensitive barley and wheat parental genotypes. The parental genotypes of these crosses also differed by at least three other traits – paraquat tolerance, leaf size, and the relative water content. These three traits were scored in two F₂populations of 80 individuals for each barley and wheat cross. Analysis of results indicated that the enhanced tolerance to paraquat was correlated with reduced leaf size and increased relative water content, two traits associated with water stress phenotypes of the drought tolerant barley and wheat parents. Our results suggested that the selection based on paraquat tolerance istechnically less demanding and thus useful for rapid screening of individuals for enhanced drought tolerance in segregating populations. This revised version was published online in August 2006 with corrections to the Cover Date.     

玉米耐旱分子育种研究进展

干旱是玉米生产的主要非生物胁迫因子之一,培育耐旱品种可以有效地保持其在干旱环境下的产量稳定性。目前,随着生物信息学数据库的不断完善及基因组学技术的发展,耐旱通用QTL的发掘以及关联分析技术在功能标记开发上的应用,新的耐旱相关转录因子／基因的克隆都为解释玉米耐旱性的复杂遗传网络和分子育种提供了新的机遇和方法。本文综述了耐旱基因组学研究进展及其在玉米耐旱分子育种上的应用。     

Molecular markers in Brassica oilseed breeding: current status and future possibilities

As PCR techniques have developed over the last 15 years, a wealth of new DNA marker technologies have arisen which have enabled the generation of high‐density molecular maps for all the major Brassica crop species. Molecular markers have also been heavily used in analyses of genetic diversity in Brassica crops. The majority of the work utilizing molecular markers in Brassica oilseed breeding has to date been based on genetic mapping using various DNA marker systems in segregating populations generated for specific investigations of particular traits of interest. For numerous qualitative traits, traditional mapping approaches have led to the development of marker‐assisted selection strategies in oilseed Brassica breeding, and in some cases to map‐based cloning of the responsible genes. For quantitative traits, however, it has become apparent that traditional mapping of quantitative trait loci (QTL) is often not sufficient to develop effective markers for trait introgression or for identification of the genes responsible. In this case, allele‐trait association studies in non‐structured genetic populations represent an interesting new approach, provided the degree of gametic phase disequilibrium between the QTL and the marker loci is sufficient. Because Brassica species represent the closest crop plant relatives to the model plant Arabidopsis thaliana, significant progress will be achieved in the coming years through integration of candidate gene approaches in crop brassicas, using the detailed information now available for the Arabidopsis genome. Integration of information from the model plant with the increasing supply of data from physical mapping and sequencing of the diploid Brassica genomes will undoubtedly give great insight into the genetics underlying both simple and complex traits in oilseed rape. This review describes the current use of available genetic marker technologies in oilseed rape breeding and provides an outlook for use of new technologies, including single‐nucleotide polymorphism markers, candidate gene approaches and allele‐trait association studies.     

非生物胁迫条件小麦根系性状的遗传学基础研究进展

作物根系与水肥利用密切相关,发掘根系性状相关遗传位点或候选基因,对于培育适宜特定土壤环境的小麦新品种具有重要意义。为系统了解低氮磷供应、盐碱、干旱等非生物胁迫对根系的影响,以及小麦根系性状遗传定位进展,本研究对近几十年相关文献进行了调研。发现尽管目前对小麦根系性状遗传解析工作已有较多报道,但许多根系性状QTL区间在不同研究间难以吻合,限制了分子标记开发和候选基因的发掘。随着高密度SNP芯片的开发及全基因组重测序技术的发展,今后整合"表型组"、"基因组"、"转录组"和"代谢组"对特定环境条件下小麦根系性状进行解析,可快速、高效地发掘特定环境条件下的优异等位变异和候选基因。本研究对于了解非生物胁迫条件小麦根系性状的遗传学基础具有参考价值。     

利用抗旱选择导入系定位向日葵产量性状QTL

干旱是造成向日葵减产的最主要因素之一。利用综合性状优良的自交系K55作为轮回亲本与抗旱自交系K58杂交构建回交导入系, 在干旱条件下进行单株产量筛选, 得到45个BC₃F₂抗旱定向选择导入系。通过全基因组SSR及SNP标记扫描, 以方差分析和基于遗传搭车原理的卡方检验对呼和浩特市及武川县两点、两种水分条件下的5个产量性状进行QTL检测。方差分析检测到的QTL根据不同环境下的表达情况分为三类, 第一类在两种水分条件下稳定表达, 包括武川的4个百粒重QTL及呼和浩特的2个单株产量QTL、3个单株实粒数QTL, 这些QTL可能对向日葵抗旱性有直接贡献; 第二类受干旱胁迫表达, 包括呼和浩特的30个和武川的27个; 第三类仅在正常供水条件下被检测到, 包括呼和浩特的38个和武川的64个。卡方检验检测到极显著位点274个。用两种方法共检测到一致性位点14个, 可能是与向日葵抗旱性相关的关键位点。本研究结果可为向日葵高效抗旱分子育种奠定基础并提供相关材料。     

Marker-assisted characterization of frost tolerance in barley (Hordeum vulgare L.)

Five molecular markers associated to two frost tolerance QTLs ( Fr-H1 and Fr-H2 ) were tested both on nine Turkish accessions, classified by breeders as highly frost-tolerant, and on a previously described sample of 26 barleys, winter, facultative and spring. Accessions were characterized in terms of frost tolerance under both field conditions and artificial freezing test at −12°C. The Turkish lines resulted to be equal or superior to the most tolerant European genotypes tested, showing that they can be used to improve the frost tolerance of the EU barley germplasm. The marker Hv BM5A ( Vrn-H1 and Fr-H1 ) resulted to be the best predictor for assisted selection within this germplasm, because of its high correlation between allelic variation and phenotypic traits. Only Hv CBF4 of the three Hv CBF markers tested at Fr-H2 was associated to the trait, but at lower significance than HvBM5A . The PCR-based molecular marker of Vrn-H1 can thus be used in barley breeding not only for selection of facultative and winter types, but also for fast routine selection of frost tolerant genotypes.