Showing papers in "Euphytica in 2015"
TL;DR: Prospects of breeding and disseminating next generation (hybrid) cultivars of arabica coffee for sustainable coffee production under changing conditions of diseases, pests and climate are discussed.
Abstract: Arabica coffees (60 % of current world coffee production) are generally sold at considerably better prices than robustas on account of superior beverage quality. However, costs of production are much higher, mainly due to more stringent demands for soil and climatic conditions, crop management, primary processing and control of several pests and diseases including the potentially very destructive coffee leaf rust (CLR) and berry disease (CBD). Breeding for disease resistance in combination with vigour, productivity and quality started in the early 1920s in India, but especially in the second half of the 20th century comprehensive breeding programmes have been implemented in several other coffee producing countries. Many of the resulting CLR- and CBD + CLR-resistant cultivars (true-breeding lines and F1 hybrids) meet the required standards of profitable and sustainable crop production. Challenges of more recent date include limited access to additional genetic resources of Coffea arabica, breakdown of host resistance to CLR, aggravating insect pest problems and the increasingly negative impact of climate change on arabica coffee production worldwide. This review discusses prospects of breeding and disseminating next generation (hybrid) cultivars of arabica coffee for sustainable coffee production under changing conditions of diseases, pests and climate. International networking on coffee breeding will facilitate sharing of resources (financial, genetic) and scientific information, application of genomics-assisted selection technologies, and pre-breeding for specific characters. Breeding and multiplication of new cultivars well adapted to the local environment will continue to be carried out at national or regional levels. A tree crop like arabica coffee does not lend itself to centralized variety development and dissemination on a global scale.
129 citations
TL;DR: A detailed genetic map is constructed and stable quantitative trait loci are detected based on an intraspecific recombinant inbred line population derived from a cross between Upland cotton cultivar/line Yumian 1 and 7235.
Abstract: Cotton fiber quality traits are controlled by multiple genes of minor effect. Identification of significant and stable quantitative trait loci (QTL) across environments and populations lays foundation for marker-assisted selection for fiber quality improvement and studies of its molecular regulation. Here, a detailed genetic map is constructed and QTL are detected based on an intraspecific recombinant inbred line population derived from a cross between Upland cotton cultivar/line Yumian 1 and 7235. A total of 25,313 SSR primer pairs, including 5,000 developed from G. raimondii BAC-ends sequences, were used to construct the genetic map which finally contained 1,540 loci, spanning 2,842.06 cM, with an average of 1.85 cM between adjacent markers. With 4 year fiber quality traits data, variance analysis revealed that they were significantly affected by genetic and environmental factors. Significant correlations were also detected between them. A total of 62 QTL were identified with combined analysis and single environment analysis. These QTL explain phenotypic variation from 5.0 to 28.1 %. For each trait, favorable alleles were conferred by both parents. Seventeen QTL were detected in more than one environment. The genetic map and stable QTL are valuable for Upland cotton genome research and breeding projects to improve fiber quality.
87 citations
TL;DR: A lack of expertise and recognition of CCNs as a factor limiting wheat production potential, combined with inappropriate breeding strategies and slow screening processes limit genetic gains for resistance to CCNs.
Abstract: Cereal cyst nematodes (CCNs) can cause significant economic yield losses alone or in combination with other biotic and abiotic factors. The damage caused by these nematodes can be enormous when they occur in a disease complex, particularly in areas subject to water stress. Of the 12 valid CCN species, Heterodera avenae, H. filipjevi, and H. latipons are considered the most economically important in different parts of the world. This paper reviews current approaches to managing CCNs via genetic resistance, biological agents, cultural practices, and chemical strategies. Recent research within the soil borne pathogen program of the International Maize and Wheat Improvement Center has focused on germplasm screening, the potential of this germplasm as sources of resistance, and how to incorporate new sources of resistance into breeding programs. Breeding for resistance is particularly complicated and difficult when different species and pathotypes coexist in nature. A lack of expertise and recognition of CCNs as a factor limiting wheat production potential, combined with inappropriate breeding strategies and slow screening processes limit genetic gains for resistance to CCNs.
70 citations
TL;DR: The SUB1 gene has been introgressed into two new popular varieties from Indonesia and the Philippines through MABC using only one backcross (BC1) with the previously developed IR64-Sub1 as the donor, presenting a promising approach to convert additional popular varieties in the future.
Abstract: Submergence is an escalating problem in many rice producing areas. A submergence tolerance gene, SUB1, derived from FR13A was previously introduced into six mega varieties through marker assisted backcrossing (MABC) with the final product selected at the BC2 or BC3 generation. Their phenotype was similar to the original varieties, but they could withstand complete inundation for up to 2 or 3 weeks. Several of these varieties have been released in South and Southeast Asia; nonetheless the development of additional submergence tolerant varieties is indispensable to provide farmers with diverse choices of varieties that are preferable for the local needs and to avoid ecological vulnerability due to planting only one variety across vast areas. To accelerate this effort, the SUB1 gene has now been introgressed into two new popular varieties from Indonesia and the Philippines, i.e. Ciherang and PSB Rc18, respectively, through MABC using only one backcross (BC1) with the previously developed IR64-Sub1 as the donor. Since this new donor is closely related to both recurrent parents, a more rapid MABC approach can be pursued due to the similarity of genetic backgrounds. Using this strategy, new submergence tolerant varieties Ciherang-Sub1 and PSB Rc18-Sub1 were developed in less than 2 years, presenting a promising approach to convert additional popular varieties in the future.
68 citations
TL;DR: 16 accessions are identified which have complete resistance and good agronomic superiority against four most prevalent races of Colletotrichum lindemutianum and may serve as useful genetic material to plant breeders for breeding bean varieties for anthracnose resistance and high yield.
Abstract: Common bean is one of the most important legume crops worldwide. Response to selection and success of hybridisation in common bean primarily depends on the nature and magnitude of genetic diversity present in the germplasm used. Germplasm comprising 4274 accessions originating from 58 countries were characterized for 22 phenotypic traits for two years. Genetic diversity for traits such as leaf length (4.5–20.7 cm), leaf width (3.4–17.5 cm), pod length (PL) (3.5–23.5 cm), no of pods/plant (4.2–59.6), seeds/pod (2.1–9.6) and 100-seed weight (SWT) (3.5–96.3 g) was observed in the accessions. Based on multivariate analysis, the entire collection was grouped into 10 genetically diverse clusters irrespective of the origin or place of collection of accessions. First three components obtained through principal component analysis explained 80.44 % of the total variance and it was contributed mainly by PL, pod width (PW), seed length (SL), seed width (SW), pods/plant and SWT. Correlation coefficient of seed weight was positively significant with leaf length, PL, PW, SL and SW while it was negatively correlated with days to flowering, pods/plant and seeds/pod. Regression analysis showed highest direct effect of SW on seed weight followed by SL, and PL. For bean anthracnose, >600 accessions showed resistance under field conditions, however when subjected to screening under artificial conditions against four most prevalent races (03, 515, 598 and 529) of Colletotrichum lindemutianum, we identified 16 accessions which have complete resistance and good agronomic superiority. These accessions may serve as useful genetic material to plant breeders for breeding bean varieties for anthracnose resistance and high yield.
63 citations
TL;DR: The results confirm that the use of GWAS is feasible for sugarcane in spite of its complex polyploid genome but also underline the need to take into account family relatedness and not only population structure.
Abstract: The objectives of the study were to assess genome wide association study (GWAS) for sugarcane on a panel of 183 accessions and to evaluate the impact of population structure and family relatedness on QTL detection. The panel was genotyped with 3327 AFLP, DArT and SSR markers and phenotyped for 13 traits related to agro-morphology, sugar yield, bagasse content and disease resistances. Marker-trait associations were detected using (i) general linear models that took population structure into account with either a Q matrix from STRUCTURE software or principal components from a principal component analysis added as covariates, and (ii) mixed linear models that took into account both population structure and family relatedness estimated using a similarity matrix K* computed using Jaccard’s coefficient. With general linear models analysis, test statistics were inflated in most cases, while mixed linear models analysis allowed the inflation of test statistics to be controlled in most cases. When only detections in which both population structure and family relatedness were correctly controlled were considered, only 11 markers were significantly associated with three out of the 13. Among these 11 markers, six were linked to the major resistance gene Bru1, which has already been identified. Our results confirm that the use of GWAS is feasible for sugarcane in spite of its complex polyploid genome but also underline the need to take into account family relatedness and not only population structure. The small number of significant associations detected suggests that a larger population and/or denser genotyping are required to increase the statistical power of association detection.
60 citations
TL;DR: The results suggest that common genetic loci may influence both of these adaptive traits and could be targeted to improve adaptation to high temperature stress.
Abstract: Cooler canopy temperatures and glaucousness have both been identified as adaptive traits for improving abiotic stress tolerance in wheat. The objective of this study was to determine if glaucousness resulting from the constitutive production of leaf cuticular waxes was associated with cooler leaf and spike temperatures under heat stress and to identify associated quantitative trait loci (QTL). A set of 121 recombinant inbred lines (RILs) derived by crossing the heat tolerant wheat cultivar ‘Halberd’ and heat susceptible wheat cultivar ‘Karl92’ was utilized for QTL mapping. Flag leaf cuticular wax was extracted and quantified using a colorimetric technique at 10 days after pollination prior to initiation of the heat stress. The parental cultivars and RIL population were then subjected to a heat treatment of 38 °C and temperature depression of both leaf and spike was measured. The parental cultivar Halberd had high flag leaf wax content, and cooler leaf and spike temperatures compared to Karl92, with the RIL population showing significant genetic variation for these traits. QTL identified for leaf and spike temperature depression and leaf waxes explained 8–12 % of the phenotypic variation. Stable QTL for leaf wax content were located on chromosomes 1B and 5A with the 5A QTL region showing localization with QTL for leaf and spike temperature depression, indicating a genetic link between these traits. The results suggest that common genetic loci may influence both of these adaptive traits and could be targeted to improve adaptation to high temperature stress.
57 citations
TL;DR: The genetic map constructed in this study is the most detailed upland cotton intraspecific map based on SSR markers to date, and could be used to construct consensus map or as reference genetic map for tetraploid cotton genome assembly.
Abstract: Cotton is a leading natural fiber crop in the textile industry worldwide. The improvement of cotton fiber quality has become more important because of changes in spinning technology and ever-increasing demands. Mapping quantitative trait locus (QTL) for fiber quality traits will enable molecular marker-assisted selection (MAS) to improve fiber quality and provide an access to reveal the molecular mechanism of fiber development. A high-density intraspecific genetic map is constructed based on an upland cotton recombinant inbred line (RIL) population. A total of 25,313 SSR primer pairs were used and yielded 1,333 polymorphic markers, with a polymorphic ratio of 5.3 %, producing 1,382 polymorphic loci in the RIL population. The map comprised 1,274 loci and spanned 3,076.4 cM with an average distance of 2.41 cM between two adjacent markers. Based on the phenotypic data of fiber quality traits from five environments, a total of 59 QTL were detected. These QTL comprised 15 QTL for fiber upper half mean length, 10 QTL for fiber length uniformity, 9 QTL for fiber strength, 10 QTL for fiber elongation and 15 QTL for fiber micronaire, respectively. The genetic map constructed in this study is the most detailed upland cotton intraspecific map based on SSR markers to date, and could be used to construct consensus map or as reference genetic map for tetraploid cotton genome assembly. Stable QTL identified across multiple environments reflect some important and favorable alleles shaping fiber quality, and they are valuable candidate alleles for MAS breeding projects as well as for gene function research related to cotton fiber development and quality improvement.
55 citations
TL;DR: Significant chickpea genomic resources have been developed and promise to increase efficiency as work to identify valuable candidate genes continues, as well as high-resolution phenotyping tools and cutting-edge technologies such as next-generation sequencing.
Abstract: Chickpea (Cicer arietinum L.) is the third most economically important food legume in the world. Its yield potential is often limited by various biotic stresses, including fungal and viral diseases, insects, nematodes and parasitic weeds. Incorporating genetic resistance into cultivars is the most effective and economical way of controlling biotic stresses and this is a major objective in many breeding programs. Extensive searches for resistances have been conducted by screening commercial varieties, landraces and closely related species. Resistances to disease such as Ascochyta blight and Fusarium wilt have been identified and molecular tools are being used to increase the efficiency of gene transfer from wild species into chickpea elite genotypes. Quantitative trait loci for resistance genes have been located on linkage maps and molecular markers associated with these loci can potentially be used for efficient pyramiding of the traits. Significant chickpea genomic resources have been developed in order to investigate resistance genes. Such resources include an integrated genetic map, expressed sequence tag libraries, bacterial artificial chromosome libraries, microarrays and draft genome sequences. Although these resources have yet to be used to improve chickpea cultivars in the field, this is likely to change in the near future. These genomic resources, as well as high-resolution phenotyping tools and cutting-edge technologies such as next-generation sequencing, promise to increase efficiency as work to identify valuable candidate genes continues.
55 citations
TL;DR: The best results were obtained with dehydration and storage in liquid nitrogen (−196 °C) with regard to in vitro germination, pollen tube length, in vivo fertilization and other variables studied, including morphological and ultrastructural integrity.
Abstract: Bromeliaceae is a large family, and many species are valued ornamentally for their bright colorful flowers. Pollen grain conservation is important for plant breeding and genetic resource conservation increasing the possibilities of crosses between allogamous species, and further hybrid production. The present study aimed to evaluate pollen conservation methodologies for Aechmea bicolor L.B.Sm. using different viability and germination tests and to characterize conservation effects in pollen morphology and ultrastructure. Pollen grains were collected from flowers at anthesis and both (flowers and pollen) were morphologically characterized. Preliminary studies were done to define the best germination medium and dehydration condition. Pollen samples were then subjected to storage under three conditions: freezer (−5 °C), ultra-freezer (−80 °C), or liquid nitrogen (−196 °C), with or without dehydration, at different intervals. In vitro germination and pollen tube length were assessed at 1, 24 h, 8, 30, 180 and 365 days. Pollen grain morphology and ultrastructure were assessed at 24 h, 30 and 365 days. The experimental design was completely randomized in a 2 × 3 + 1 factorial design (2 dehydration conditions, 3 storage conditions, and 1 control). The plot was subdivided by storage time with plots defined by the factorial design, and subplots by storage time and their interaction with plot treatments. The best results were obtained with dehydration and storage in liquid nitrogen (−196 °C) with regard to in vitro germination, pollen tube length, in vivo fertilization and other variables studied, including morphological and ultrastructural integrity. Fruits produced developed normally and produced viable seeds, with germination rates above 92 %.
54 citations
TL;DR: The assessed population presenting genetic variability and the superior individuals for each trait were identified, thus enabling the continuity of the selective process and the analyses by the REML/BLUP methodology and the presented model proved adequate for gain prediction, with good genetic breeding perspectives.
Abstract: The restricted maximum likelihood/best linear unbiased prediction (REML/BLUP) method involves, simultaneously, the estimation of variance components and the prediction of the genetic values, considering the optimum procedure to make inferences in genetic and non-phenotypic levels. By using the mixed models methodology, this study aimed to estimate genetics parameters and genotypic values in a segregating population comprising 118 individuals from Passiflora interspecific crossing. The experiment was arranged in randomized block design with two repetitions. The traits number of fruits, level of soluble solids and pulp mass presented large genetic variability, a fact that contributed to high heritability estimations and selective accuracy, and revealed excellent possibilities to the selection and breeding of Passiflora segregating populations. By comparing the average of the 30 selected genotypes with the general average of the population, it was possible to observe higher gain estimations for the number of fruits (319.15 %) and pulp mass (73.12 %), lower gains for fruit mass (21.50), soluble solids level (13.43), longitudinal fruit diameter (6.32) and transverse fruit diameter (4.99) as well as low reductions in shell thickness (−0.0036) and length of the androgynophore (0.0056), in relation to the first ordinated individuals. The assessed population presenting genetic variability and the superior individuals for each trait were identified, thus enabling the continuity of the selective process. The analyses by the REML/BLUP methodology and by the presented model proved adequate for gain prediction, with good genetic breeding perspectives.
TL;DR: Resistance to salt stress, powdery mildew and to both stresses combined in tomato using the Solanum habrochaites LYC4 introgression line (IL) population increases the understanding of the genetic regulation of responses to abiotic and biotic stress combinations and can provide leads to more efficiently breeding crops with a high level of disease resistance while maintaining their performance in combination with abiotic stress.
Abstract: Abiotic and biotic stress factors are the major constrains for the realization of crop yield potential. As climate change progresses, the spread and intensity of abiotic as well as biotic stressors is expected to increase, with increased probability of crops being exposed to both types of stress. Shielding crops from combinatorial stress requires a better understanding of the plant’s response and its genetic architecture. In this study, we evaluated resistance to salt stress, powdery mildew and to both stresses combined in tomato, using the Solanum habrochaites LYC4 introgression line (IL) population. The IL population segregated for both salt stress tolerance and powdery mildew resistance. Using SNP array marker data, QTLs were identified for salt tolerance as well as Na+ and Cl− accumulation. Salt stress increased the susceptibility of the population to powdery mildew in an additive manner. Phenotypic variation for disease resistance was reduced under combined stress as indicated by the coefficient of variation. No correlation was found between disease resistance and Na+ and Cl− accumulation under combined stress Most genetic loci were specific for either salt stress tolerance or powdery mildew resistance. These findings increase our understanding of the genetic regulation of responses to abiotic and biotic stress combinations and can provide leads to more efficiently breeding tomatoes and other crops with a high level of disease resistance while maintaining their performance in combination with abiotic stress.
TL;DR: Three M-QTLs were identified as relatively more important for molecular breeding and will facilitate further work on genetic architecture and cloning of QTLs for grain traits including grain weight.
Abstract: Common wheat is unique in providing a large number of diverse end-products, including chapati, biscuits, bread and noodles. Grain weight and other grain traits contribute to grain yield and milling quality. Many earlier QTL studies reported at least 332 QTLs for grain traits including grain weight. We conducted a QTL analysis (composite interval mapping) of grain traits using a set of 92 recombinant inbred lines (RILs) derived from a cross between Rye Selection 111 (superior grain traits) and Chinese Spring (inferior grain traits). Forty-five QTLs for six grain traits, on 19 of the 21 chromosomes (except 2D and 3D) were identified. Nineteen of these QTLs, each for 2–3 traits were located on six chromosomes (2A, 3B, 6B, 6D, 7A and 7D). The pleiotropic nature or tight linkage of QTLs controlling different correlated traits (except the one on 6DS) was confirmed by joint MCIM. Meta-QTL (M-QTL) analysis of grain traits (including grain weight) was conducted using earlier reported QTL results (including QTLs reported in the present study). From this analysis, 23 M-QTLs were identified on eight chromosomes. These results were compared with those of our current QTL analysis and previous studies; three M-QTLs were identified as relatively more important for molecular breeding and will facilitate further work on genetic architecture and cloning of QTLs for grain traits including grain weight.
TL;DR: NAUH164, produced from ethyl methyl sulfonate treatment of wheat variety Sumai 3, has reduced plant height and shortened spike length and has an atypical vascular bundle arrangement and overall smaller cell volumes.
Abstract: Plant height and spikelet density are important agronomic traits related to plant architecture and grain yield in wheat. The development of wheat mutants not only provided new genetic resources for wheat improvement, but also facilitated our understanding of the regulation of these traits at the molecular level. Here, we report the identification of a dwarf mutant with a compact spike. NAUH164, produced from ethyl methyl sulfonate treatment of wheat variety Sumai 3, has reduced plant height and shortened spike length. Microscopic observations showed that the mutant has an atypical vascular bundle arrangement and overall smaller cell volumes. Sensitivity of seedlings to exogenous gibberellin was not changed, and plant height was not restored to the level of the wildtype. Dwarfness and compact spike were controlled by a single dominant gene that was designated Rht23, which was mapped 4.7 cM distal to SSR marker Gdm63 and 11.1 cM proximal to Barc110 on chromosome 5DL. Comparative sequence analysis of the co-linear regions in common wheat and Aegilops taushii indicated that Rht23 occurs in a physical interval of 8.5 Mb.
TL;DR: This work provides a comprehensive and accurate method for evaluating chilling tolerance in tomato.
Abstract: Tomato is one important vegetable but with low chilling tolerance Though research on tomato chilling tolerance has been reported, the evaluation method has not identified In the present study, seedlings of 48 tomato lines were treated with chilling stress (4/4 °C, day/night) for 8 days, and the chilling injury index (CII) was then determined Four physiological indexes including electrolyte leakage, total chlorophyll (Chl) content, the chlorophyll fluorescence parameters Fv/Fm and ΦPSII were measured in leaves of tomato seedlings before and after the treatment It was found that CII, and the electrolyte leakage increased, while the total Chl content, Fv/Fm, and ΦPSII decreased in response to chilling stress Based on the chilling tolerance coefficients (CTCs) of four physiological indexes, the comprehensive evaluation value (D) of each tomato line was calculated by principal component analysis (PCA), and subordinate function analysis The D value had significant correlation with CIIs and CTCs of the physiological indexes, which suggested that D value could accurately predict the chilling tolerance of tomato lines Based on the D values, 48 tomato lines could be divided into four groups by cluster analysis: chilling-tolerant (15 lines), medium chilling-tolerant (21 lines), low chilling-tolerant (seven lines), and chilling-sensitive (five lines) Meanwhile, linear equation was constructed Therefore, this work provides a comprehensive and accurate method for evaluating chilling tolerance in tomato
TL;DR: This study clearly advances the knowledge on genetic controls of plant height, lodging and maturity in soybean, and identifies more efficient and reliable markers for MAS for these traits than those currently exist.
Abstract: Soybean (Glycine max L. Merr.) is a major crop and a leading source of protein meal and edible oil worldwide. Plant height (PHT), lodging (LDG), and days to maturity (MAT) are three important agronomic traits that influence the seed yield of soybean. The objective of this study was to map quantitative trait loci (QTL) for PHT, LDG and MAT using a high density SNP map of a recombinant inbred line soybean mapping population. With single factor analysis of variance six, four, and three QTL were identified across environments for PHT, LDG, and MAT, respectively. Several QTL for each trait were also detected by composite interval mapping with high confidence. Two and one QTL for PHT and LDG, respectively were novel QTL identified in this study. Additionally, most QTL identified in the present study are flanked by two or more SNP markers that are closely linked to each QTL. The SNP markers identified to be closely linked to each QTL in this study are valuable for marker assisted selection (MAS) of the QTL by interested soybean breeding programs. Thus, this study clearly advances the knowledge on genetic controls of plant height, lodging and maturity in soybean, and identifies more efficient and reliable markers for MAS for these traits than those currently exist.
TL;DR: Tolerance to mechanical transmission of ToLCNDV was identified in melon, within Cucumis melo subsp.
Abstract: Cucurbits are major crop species, including fruits and vegetables cultivated worldwide that supply essential vitamins and minerals to current diets in developed and developing countries. Viral diseases are main factors affecting cucurbits cultivation. The most widespread and damaging have been aphid-borne viruses belonging to the Potyviridae family. Whitefly-transmitted begomoviruses (Geminiviridae) have been identified more recently in different cucurbit species. A severe outbreak of Tomato leaf curl New Delhi virus (ToLCNDV) occurred in pumpkins and melons in the main production area of Southern Spain in 2012–2014. We developed a mechanical inoculation method to facilitate the screening of germplasm against this virus. Mechanical transmission with this method was confirmed in 4 genera and 13 species of the family, including the main crops, cucumber, melon, watermelon and pumpkins, and also crop-related exotic germplasm (landraces and wild species) used for cucurbits breeding. Diversity in the response was observed within and among species. Tolerance to mechanical transmission of ToLCNDV was identified in melon, within Cucumis melo subsp. agrestis var. momordica and in wild agrestis accessions. All the tolerant accessions came from India, the country in which this virus was firstly reported. Some of these accessions have been previously reported to be tolerant or resistant to other viruses and as they are fully crossable to commercial melons, they are good sources to develop new melon varieties with tolerance to ToLCNDV.
TL;DR: Identifying genomic regions responsible for grain yield (GY) under WDS will aid in understanding the genetics of drought tolerance (DT) and development of DT cultivars and fine mapping of the major QTLs on chromosome 3BS will enable identification of robust markers and candidate genes for marker-assisted breeding for DT in wheat.
Abstract: Water deficit stress (WDS) is a serious constraint to wheat productivity in rain-fed and limited irrigation environments. Identifying genomic regions responsible for grain yield (GY) under WDS will aid in understanding the genetics of drought tolerance (DT) and development of DT cultivars. A population of 206 recombinant inbred lines derived from WL711/C306 was phenotyped for GY and related traits under water deficit and irrigated conditions in seven different environments to identify genomic regions associated with eleven yield related traits. Both the parents contributed positive alleles for the traits studied. A novel genomic region for GY under WDS, qGYWD.3B.1 was detected on chromosome 3BS of wheat. The yield enhancing allele under drought stress at this locus was contributed by DT parent C306. This genomic region explained 18.7 % of phenotypic variation for GY under WDS and co-located with genomic regions for GY components. Another novel, consistent genomic region for GY under WDS, qGYWD.3B.2 explained 19.6 % of phenotypic variation with positive allele coming from drought susceptible parent WL711. A novel genomic region for drought susceptibility index for GY, qDSIGY.4A.1 was consistently detected in six of seven environments explaining 15.6 % of phenotypic variation. Other important genomic regions for GY and biomass under WDS were mapped on chromosomes 7BL and 6AS, respectively. Fine mapping of the major QTLs on chromosome 3BS will enable identification of robust markers and candidate genes for marker-assisted breeding for DT in wheat.
TL;DR: The results showed that Verticillium wilt resistance was successfully introduced into the cultivated eggplants, and the agronomic traits of the interspecific hybrid progeny were improved by continuous backcrossing with the cultivated Eggplants.
Abstract: Verticillium wilt, caused by Verticillium dahliae, is a soil-borne disease of the cultivated eggplant (Solanum melongena). The accession PI388846 from a wild species S. linnaeanum, shows resistance to Verticillium wilt. The introgression of its disease resistance gene into cultivated eggplants would allow for breeding disease resistant eggplants. In this study, interspecific hybridization and subsequent backcrossing between PI388846 and cultivated eggplants were performed. The results showed that Verticillium wilt resistance was successfully introduced into the cultivated eggplants, and the agronomic traits of the interspecific hybrid progeny were improved by continuous backcrossing with the cultivated eggplants. In addition, a gene specific marker for the Ve homolog in PI388846 was developed to detect Verticillium wilt resistance in the backcross population. The results represent a positive beginning for the genetic enhancement of cultivated eggplants for Verticillium wilt resistance.
TL;DR: The QTLs identified through linkage and association mapping may be useful for marker-assisted selection in rice breeding programs and may accelerate the development of salt-tolerant rice varieties.
Abstract: Soil salinity is a major constraint to rice production. Na+ and K+ concentrations and ion balance play important roles in the salt tolerance of rice. In the present study, linkage mapping and association mapping were used to identify the QTLs for the visual tolerance score (SES), and the concentrations of Na+ and K+ in shoots (SNC and SKC) and roots (RNC and RKC). A BC2F2:3 population with 137 SSR markers derived from Dongnong425 (a salt-sensitive and widely cultivated variety) as the recurrent parent and Changbai10 (a salt-tolerant variety) as the donor parent was used for linkage mapping. A total of 13 QTLs were identified by the inclusive composite interval mapping method, including 2 for SES, 4 for SNC, 3 for SKC, 3 for RNC, and 1 for RKC. This study was supplemented with association mapping, which was conducted using a panel of 341 japonica rice accessions from different geographical origins with 160 selected SSR markers. A total of 24 significant marker-trait associations (P ≤ 0.01) involving 20 markers were identified using the GLM (Q) and MLM (Q+K) models in TASSEL2.1. Among them, 10 of the SSR markers confirmed or narrowed the genomic regions for salt tolerance that were reported in linkage studies, including six QTLs identified during the present study. The QTLs identified through linkage and association mapping may be useful for marker-assisted selection in rice breeding programs and may accelerate the development of salt-tolerant rice varieties.
TL;DR: A genetic map to determine lycopene content and other horticultural fruit traits using a F2 population developed from a cross between the two lines of watermelon LSW-177 and Cream of Saskatchewan and 12 QTLs for all of the traits measured are constructed.
Abstract: Lycopene content is an important factor for determining watermelon fruit quality. However, the low DNA polymorphism among cultivated watermelon (Citrullus lanatus) has hindered the ability to establish high quality genetic maps and study the quantitative trait loci (QTL) controlling the lycopene content trait. In this study, we successfully constructed a genetic map of watermelon to determine lycopene content and other horticultural fruit traits using a F2 population developed from a cross between the two lines of watermelon LSW-177 and Cream of Saskatchewan. The genetic map contained 16 linkage groups covering a total length of 2,039.5 cM, which included 37 SSRs (Simple Sequence Repeat) and 107 CAPSs (Cleaved Amplified Polymorphic Sequences), with all of the CAPS markers developed from high-throughput re-sequencing of data from this study. Three CAPS markers (WII04E07-33,WII04E07-37,WII04E07-40) caused the F2 population to perfectly co-segregate for each F2 population plants. We also obtained 12 QTLs for all of the traits measured. Only one QTL (LCYB4.1) was detected with a high value of trait variation (83.50 %) that related to lycopene content and mapped on Chromosome 4 between CAPS markers WII04E07-33 and WII04E07-40, which could nearly account for all of the differences in lycopene content between the two parental strains. In this study, we highlighted 2,458 CAPS loci that were suitable for primer design with a polymorphism of 48.9 %, which is approximately a 12-fold increase from previous studies. The present map and QTLs will facilitate future studies on determining lycopene content related genes and cloning watermelon genes, while also providing for useful markers for breeding for lycopene content.
TL;DR: Strong correlation between grain yield, canopy biomass and harvest index across environments suggested that canopy biomassand harvest index are repeatable and reliable plant traits to determine drought resistance in common bean.
Abstract: Common bean (Phaseolus vulagaris L.) is mainly produced in Latin America, and Eastern and Southern Africa where seasonal rainfall is erratic and soil moisture deficit often limits its production. The objectives of this study were to identify superior advanced small red common bean lines with better grain yield under drought, and to identify plant traits that could serve as selection criteria for evaluating drought resistance. Thirty four advanced inbred lines were developed through triple cross and evaluated with two commercial checks (Nasir and Red Wolayita) under drought and irrigated field conditions in two seasons (2009 and 2010) and at two locations (Melkassa and Doni Kumbi Farm) in Ethiopia. Grain yield, pods/plant, seeds/plant and 100 seed weight were reduced by 47, 19, 15, and 9 %, respectively, under the drought conditions compared to the irrigated conditions. Seven genotypes (L62, L5, L20, L79, L12, L41, and L83) had better yield under drought compared to the standard check. Similarly, these genotypes had better predicted genotypic effects, suggesting that they would also be useful as drought resistant donors in common bean cultivar development program. Genotypic variance expressed as proportions to phenotypic variance was higher compared to genotype × environment interaction effects for all traits under drought conditions, suggesting that these genotypes can be used to further improve drought-resistance regardless of environments. Strong correlation between grain yield, canopy biomass and harvest index across environments suggested that canopy biomass and harvest index are repeatable and reliable plant traits to determine drought resistance in common bean.
TL;DR: The results indicated that the efl-1 gene identified from ICCV 2 was also present in ICCV 96029, which has ICCV2 as one of the parents in its pedigree.
Abstract: Flowering time and crop duration are the most important traits for adaptation of chickpea (Cicer arietinum L.) to different agro-climatic conditions. Early flowering and early maturity enhance adaptation of chickpea to short season environments. This study was conducted to establish allelic relationships of the early flowering genes of ICC 16641, ICC 16644 and ICCV 96029 with three known early flowering genes, efl-1 (ICCV 2), ppd or efl-2 (ICC 5810), and efl-3 (BGD 132). In all cases, late flowering was dominant to early-flowering. The results indicated that the efl-1 gene identified from ICCV 2 was also present in ICCV 96029, which has ICCV 2 as one of the parents in its pedigree. ICC 16641 and ICC 16644 had a common early flowering gene which was not allelic to other reported early flowering genes. The new early flowering gene was designated efl-4. In most of the crosses, days to flowering was positively correlated with days to maturity, number of pods per plant, number of seeds per plant and seed yield per plant and negatively correlated or had no correlation with 100-seed weight. The double-pod trait improved grain yield per plant in the crosses where it delayed maturity. The information on allelic relationships of early flowering genes and their effects on yield and yield components will be useful in chickpea breeding for desired phenology.
TL;DR: A genetic linkage map and mapping QTL for fiber quality was constructed and these major QTLs were stable and especially useful for marker assisted selection to improve fiber quality in Upland cotton.
Abstract: Cotton fiber is widely used as the raw materials for the textile industry. With the development inspinningtechnology,theimprovementofcottonfiber quality is becoming more and more important. How- ever, negative correlation between yield and fiber quality is an obstacle for cotton improvement. Mole- cular marker assisted selection provides a potential methodology to break the negative correlation. The main objective of this research was to construct a geneticlinkagemapandmappingQTLforfiberquality,
TL;DR: Positive correlation was found between root traits and plant height in both populations and root traits was found unaffected by Rht2 gene.
Abstract: A well organized root system is of great importance in plants for better anchorage and efficient nutrient use. Two wheat populations were used to map QTLs associated with root traits. A double haploid population contains 216 lines and derived from a cross between Nongda 3338 and Jingdong 6. The RIL progeny includes 217 lines which were evolved from another cross between Nongda 3331 and Zang 1817.
Root morphological parameters were measured in seedling stage using hydroponic culture technique. Total root length, root surface area, root volume, number of root tips and main root length were measured for both the populations. In total, 54 QTLs for root traits were detected. Among the QTLs detected, 39 QTLs distributed on chromosomes 2A, 2B, 3A, 4B, 4D, 5A, 6A, 6D, and 7B were identified in DH population, while 15 QTLs on chromosomes 1B, 2B, 3B, 4A, 4D, 5A, 5B and 7A were identified in the RIL population. QTLs were clustered in 8 genomic regions in DH and 4 genomic regions in RIL population. Important QTL rich regions on chromosome 2A (wsnp_Ex_c19516_28480622-Xgwm614b), 3A (Excalibur_c24354_465-Kukri_rep_c102151_697 and Xwmc695-IAAV5821) and 4D (RAC875_c5827_554-wsnp_BF473052D_Ta_2_1) in DH and 3B (Xbarc115-Xwmc291), 4A (Xcwem34-Xbarc28b) and 4D (Xbarc1118-Rht2) in RIL population were found as they had pleiotropic effect for controlling root traits. Negative correlation was found between root traits and plant height in both populations. Root traits was found unaffected by Rht2 gene. Major QTLs detected on chromosome 4D for root traits might be different from the QTL detected previously for plant height.
TL;DR: A physical map was constructed based on the recent Brassica napus genome release and used link QTL for resistance to S. sclerotiorum in B. napus to identify clusters of nucleotide-binding-site, leucine-rich-repeat-containing candidate resistance genes.
Abstract: Much research has identified quantitative trait loci (QTL) for resistance to Sclerotinia sclerotiorum in Brassica. However, the real-world applicability of these QTL for gene discovery and resistance breeding has been hampered by poor inter-study integration. This is due to the use of different mapping populations, environments and diverse markers. In this study, a physical map was constructed based on the recent Brassica napus genome release and used link QTL for resistance to S. sclerotiorum. In total, 353 markers, divided into 146 and 207 on the A and C genomes respectively, were used. This enabled integration of 35 QTLs, including 8 leaf resistance (LR) and 27 stem resistance (SR) QTLs. SR QTLs that were conserved across studies were found on A9 (from 22.5 to 27.5 Mb) and on C6 (from 29.5 to 36.1 Mb). Clusters of nucleotide-binding-site, leucine-rich-repeat-containing candidate resistance genes were identified, which provide key targets for identification of genes for resistance to S. sclerotiorum in B. napus.
TL;DR: It is predicted that the lodging risk of varieties introduced since 2000 are likely to have increased due to further increases in yield potential and the absence of further shortening, as well as possible reasons why UK plant breeders have not continued to shorten wheat.
Abstract: The relationship between crop height and yield is complex with genes and genetic markers for greater height associated with both increases and decreases in yield. As a result of this the optimum height for maximum potential yield is not well understood and has been estimated at between 70 and 100 cm. This study investigated the effect of plant breeding on the height of UK winter wheat varieties by analysing data on straw shortness scores and absolute height collected from UK national variety testing trials between 1977 and 2013. The analysis showed that varietal introductions between the early 1970s and 1980 shortened plant height by approximately 15 cm (110–95 cm) followed by a gradual reduction to about 88 cm by the 1990s. There was no significant trend in height between 1990 and 2013. It was estimated that the reduction in plant height between 1970 and 2000 would have been sufficient to counteract the increase in lodging risk caused by the increase in yield potential of new varieties over this period of approximately 3 t/ha. It is predicted that the lodging risk of varieties introduced since 2000 are likely to have increased due to further increases in yield potential and the absence of further shortening. Possible reasons why UK plant breeders have not continued to shorten wheat are considered.
TL;DR: The present review emphasizes the mode of sex determination among dioecious plants vis-a-vis summarizes the works related to gender specific markers generated using male and female plants from agriculturally important dioemious crops.
Abstract: Flowering plants are known to exhibit vast diversity of sexual systems encompassing bisexual, monoecious and dioecious conditions. Dioecy offers opportunities to explore separately the male and female programmes giving an insight to the evolutionary, developmental and molecular processes leading to separate mechanisms for sex expression. Mechanisms controlling sex can either be genetic or epigenetic (physiological and environmental). Plant hormones too influence sex expression. An active Y sex determination system and an X to autosomes ratio systems are common amongst the flowering plants. Advances in our understanding of sex determination has been addressed both by conventional as well as molecular approaches. Using conventional techniques mainly cytogenetics, sex chromosomes in some dioecious plants have been identified and characterized. Surprisingly, the presence of well defined sex chromosomes was found in only few species. Some sex linked genes have also been identified and characterized using molecular approaches but none of these genes have a direct link to sex determination. Molecular markers have been employed to resolve the enigma associated with dioecism to a certain extent. Its application in plant breeding is immensely beneficial. Positively, it would be beneficial for validation of sex prior their sex expression at larger perspectives. The present review therefore emphasizes the mode of sex determination among dioecious plants vis-a-vis summarizes the works related to gender specific markers generated using male and female plants from agriculturally important dioecious crops.
TL;DR: The major QTLs identified here are expected to provide useful information toward understanding the genetic mechanisms of important agronomic traits related to yield in sorghum.
Abstract: In recent years, sorghum (Sorghum bicolor (L.) Moench) has gained attention as a food, feed, and biofuel crop, but yield improvements have lagged behind those in other crops. Here, we investigated quantitative trait loci (QTLs) associated with yield and yield-related traits in sorghum. We measured eight morphological traits related to yield potential in an F2 and F2:3 population derived from a cross between African and Japanese sorghum landraces, and we developed a genetic linkage map of 137 sorghum genome-based simple sequence repeat markers. The total map length was 1,239.2 cM, with an average distance of 9.9 cM between adjacent markers. By using both single- and multiple-QTL approaches to identify the chromosomal regions controlling these traits, we identified a total of 52 QTLs associated with the eight traits (culm length, number of tillers, panicle length, culm diameter, leaf length, leaf width, grain weight/panicle, and 100-grain weight) using F2 phenotypic values while 25 QTLs were confirmed in the F2:3 population. The percentage phenotypic variation explained by individual QTLs ranged from 3.1 to 36.3 % in the F2 and 2.1 to 30.4 % in the F2:3 population. Most of the traits were significantly correlated with one another (P < 0.05). Ten QTLs had a significant association with more than one trait. A QTL for culm length was mapped to the same region of chromosome 7 as the dw3 gene for plant height. The major QTLs identified here are expected to provide useful information toward understanding the genetic mechanisms of important agronomic traits related to yield in sorghum.
TL;DR: A differential set of ten Genetically Modified (GM) plants harboring single late blight R genes in the same genetic background (Desiree) was found that the GM Desiree differential set was more accurate for isolate virulence typing than the conventional (extended) differential set.
Abstract: Late blight is an important disease in potato that is caused by the oomycete Phytophthora infestans. In the past, Solanum demissum late blight resistance (R) genes were introgressed into cultivated potato (Solanum tuberosum). Eleven of these resistant plants were selected to characterize the virulence spectrum of individual P. infestans isolates and to monitor the dynamics of virulence in P. infestans populations. These plants are referred to as the Mastenbroek and Black differential sets. It has long been assumed that each differential plant contained one single R gene. In the current study and previous studies, however, most Mastenbroek differential plants were shown to harbor multiple R gene(s), which blurs virulence typing of late blight isolates. In order to acquire more accurate virulence profiles, we extended the Mastenbroek differential set with Solanum spp. plants harboring reduced R gene complexity and with plants containing recently identified R genes from related but different Solanum species. In addition, a differential set of ten Genetically Modified (GM) plants harboring single late blight R genes in the same genetic background (Desiree). By analyzing the virulence spectra of recently collected isolates using both newly described differential sets, we found that the GM Desiree differential set was more accurate for isolate virulence typing than the conventional (extended) differential set. Besides, the GM Desiree differential set was shown to be useful as trap plants to isolate novel P. infestans strains and to monitor virulence towards particular R genes in P. infestans populations `on site´. Legislative restrictions are, however, limiting the use of the GM Desiree differential set.