QTL analysis of morphological traits in a tomato recombinant inbred line population.

Quantitative trait loci (QTLs) influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RILs) derived from a cross of the cultivated tomato Lycopersicon esculentum with a related wild species, Lycopersicon cheesmanii. One hundred and thirty-two RFLP loci spaced throughout the tomato genome were used as DNA probes on genomic DNA from 97 RIL families. Morphological traits, including plant height, plant fresh mass, number of branches, number of nodes, first flower-bearing node, and leaf length, were evaluated in two controlled environment trials in 1992 and 1993. QTLs were detected via regression analyses at multiple marker loci for each morphological trait. A total of 41 markers were significantly associated with the traits examined. Large additive effects were measured at many of these loci. QTLs for multiple traits were detected on chromosomes 3 (TG74) and 4 (CT188), suggesting the possible association of these chromosome segments with genes controlling growth and development in tomato. These chromosomal regions were also associated with multiple morphological traits in a L. esculentum x Lycopersicon pennellii cross. A total of 13% of the QTLs identified for traits common to both studies occupied similar map positions.     

Zinc fertilization and water stress affects plant water relations, stomatal conductance and osmotic adjustment in chickpea (Cicer arientinum L.)

Chickpea (Cicer arietinum) is an important dryland pulse crop in many parts of the world. Productivity is often limited by periods of water deficit and in a number of regions zinc deficiency occurs, but the interaction between zinc nutrition and water stress has not been studied extensively. This interaction was examined in two glasshouse experiments. Chickpea was grown under deficient (no applied Zn) or adequate (2.5 μg Zn/g soil) levels of zinc in pots for either 53 days (Experiment 1) or 40 days (Experiment 2) before being exposed to a single period of water stress that lasted for 12 days (Experiment 1) or 23 days (Experiment 2). In one experiment four genotypes (Tyson, ICC-4958, T-1587 and NIFA-88) differing in their sensitivity to zinc deficiency were compared during a single drying cycle, and in the second experiment a single cultivar (Tyson) was compared under well-watered and water stress conditions. Water stress was induced by allowing the soil to dry gradually and the responses in shoot biomass, water use, plant water relations and carbon isotope discrimination (Δ, ‰) were measured. Shoot biomass, water use and water use efficiency were reduced by zinc deficiency. Stomatal conductance was lower in zinc-deficient plants as well. Zinc deficiency reduced Δ by about 1‰ and there were significant differences in Δ between genotypes which were independent of the level of zinc nutrition. At an adequate level of zinc there was a significant negative correlation between Δ and shoot biomass and between Δ and water use efficiency among the four chickpea genotypes, but these correlations were not significant under zinc deficiency. Osmotic potential was lower and turgor higher in the leaves of zinc-deficient plants, but the ability to adjust osmotically was reduced by zinc deficiency as stress developed. In conclusion, zinc-deficiency reduced the efficiency with which the water was used for biomass production and compromised the plant’s capacity to respond to water stress by osmotic adjustment.     

A gene for leaf necrosis in chickpea (Cicer arietinum L.)

Necrosis of leaves was observed in the glabrous mutant (ICC 15566) of desi chickpea (Cicer arietinum L.). It was characterized by drying of leaflet margins to drying of complete leaflets of older leaves. The oldest leaves were the most affected and the intensity of necrosis decreased toward the apical meristem. A single recessive gene, designated nec, was found to govern the necrotic characteristic. The nec locus was linked to gl (glabrous shoots) with a map distance of 16 +/- 3 cM. The loci slv (simple leaves), mlv (multipinnate leaves), nlv (narrow leaflets), hg (prostrate growth habit), P (pink corolla), and shp (round seed shape) segregated independently of nec.     

Multi-environment QTL mapping in blackcurrant (Ribes nigrum L.) using mixed models

The first genetic linkage map of blackcurrant, published by Brennan et al. (Euphytica 161:19–34, 2008), identified regions where quantitative trait loci (QTLs) for some important traits were located. The analysis was complicated by the fact that the mapping population was found to contain two subgroups, with segregation ratios consistent with these being crossed and selfed offspring. The QTL analysis was based on the trait mean over 3 years and focused on the crossed offspring. Here we proposed a mixed model multi-environment approach for this population. The 3 years are considered as three separate environments, the data from both the selfed and crossed offspring are combined and different residual terms are explored to model the correlation between the years. This permits tests for interactions between the QTLs, the year and the type of offspring (selfed or crossed). This is applied to re-analyse two important traits, anthocyanin concentration and budbreak. Several additional QTLs were identified, some affecting the trait in both the selfed and crossed offspring, others in just one.     

Resistance to beet armyworm in a chickpea recombinant inbred line population

Beet armyworm, Spodoptera exigua (Hübner), is an economic pest of chickpea, Cicer arietinum L., in Mexico and the Indian subcontinent. Larvae feed on the vegetative and reproductive stages of chickpea and the development of plant resistance is a priority in the management of this pest. Forty‐two recombinant inbred lines (RILs) from a chickpea recombinant inbred line population (CRIL‐7) developed from a cross between FLIP 84‐92C (susceptible C. arietinum) and PI 599072 (resistant C. reticulatum Lad. accession) were rated resistant (nine lines with post‐trial larval weights 0.42–0.59 mg), moderately resistant/susceptible (25 lines, larval weights 0.61–0.99 mg) and susceptible (eight lines, larval weights 1.01–2.17 mg) to beet armyworm larvae in a general glasshouse screening. Resistance and susceptibility of entries (RILs in the CRIL‐7 population, parents, checks) was based on the average weight gain and fate of early‐stage larvae on pre‐flowering plants. In a growth chamber trial, early‐instar larval weight gain differed significantly (P < 0.0001) among entries (12 RILs, parents, checks), with mean weights from 0.80 mg (resistant RIL) to 4.03 mg (susceptible kabuli cultivar). There were no significant differences (P = 0.0836) in larval mortality among the entries in the growth chamber trial, although mortality rates were 28.2–61.9%. Flavonoid and isoflavonoid extractions and analyses did not clarify the role played by these phytochemicals in chickpea resistance to S. exigua. The requisite high levels of resistance to S. exigua and other pests for breeding resistant culivars may reside in the CRIL‐7 population.     

Relationship between P and Mn in chickpea (Cicer arietinum L.)

Summary Phosphorus and Mn relationship was studied in chickpea at two stages of growth in pot culture using 0, 7.5, 15 and 30 ppm P and 0, 5, 10 and 15 ppm Mn. The dry matter yield increased with P at both stages of growth. Manganese improved the yield only in the first stage. Initial levels of Mn enhanced while higher levels had a depressing effect on tissue P. Addition of 7.5 ppm P enhanced Mn concentration at first stage and at higher levels a marked reduction in Mn content was observed at both the stages.     

Plant regeneration via somatic embryogenesis in chickpea (Cicer arietinum L.)

Efficient plant regeneration via somatic embryogenesis has been developed in chickpea cultivar C235. Leaf explants, on MS medium supplemented with 1.25 mg/l 2,4-D and 0.25 mg/l kinetin, yielded somatic embryos with high efficiency during dark incubation. MS medium supplemented with B₅ vitamins, 0.125 mg/l IBA and 2 mg/l BAP was found suitable for embryo maturation. The well formed embryos germinated into plantlets on basal B₅ medium supplemented with 0.25 mg/l BAP. Further development into healthy plantlets was obtained on basal B₅ medium. Hardened plantlets produced normal, fertile plants upon transfer to soil.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - BAP 6-Benzyl-aminopurine - IAA IndoIe-3-acetic acid - IBA Indole-3-butyric acid - NAA 1-Naphthalene acetic acid - Kinetin 6-furfuryl aminopurine - Zeatin 6-(4-hydroxy-3-methylbut-2-enylamino)-purine     

Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.)

Background

Upland cotton (Gossypium hirsutum L.) accounts for about 95% of world cotton production. Improving Upland cotton cultivars has been the focus of world-wide cotton breeding programs. Negative correlation between yield and fiber quality is an obstacle for cotton improvement. Random-mating provides a potential methodology to break this correlation. The suite of fiber quality traits that affect the yarn quality includes the length, strength, maturity, fineness, elongation, uniformity and color. Identification of stable fiber quantitative trait loci (QTL) in Upland cotton is essential in order to improve cotton cultivars with superior quality using marker-assisted selection (MAS) strategy.

Results

Using 11 diverse Upland cotton cultivars as parents, a random-mated recombinant inbred (RI) population consisting of 550 RI lines was developed after 6 cycles of random-mating and 6 generations of self-pollination. The 550 RILs were planted in triplicates for two years in Mississippi State, MS, USA to obtain fiber quality data. After screening 15538 simple sequence repeat (SSR) markers, 2132 were polymorphic among the 11 parents. One thousand five hundred eighty-two markers covering 83% of cotton genome were used to genotype 275 RILs (Set 1). The marker-trait associations were analyzed using the software program TASSEL. At p < 0.01, 131 fiber QTLs and 37 QTL clusters were identified. These QTLs were responsible for the combined phenotypic variance ranging from 62.3% for short fiber content to 82.8% for elongation. The other 275 RILs (Set 2) were analyzed using a subset of 270 SSR markers, and the QTLs were confirmed. Two major QTL clusters were observed on chromosomes 7 and 16. Comparison of these 131 QTLs with the previously published QTLs indicated that 77 were identified before, and 54 appeared novel.

Conclusions

The 11 parents used in this study represent a diverse genetic pool of the US cultivated cotton, and 10 of them were elite commercial cultivars. The fiber QTLs, especially QTL clusters reported herein can be readily implemented in a cotton breeding program to improve fiber quality via MAS strategy. The consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying fiber development.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-397) contains supplementary material, which is available to authorized users.     

Agrobacterium mediated transformation of chickpea (Cicer arietinum L.) embryo axes

 Embryo axes of four accessions of chickpea (Cicer arietinum L.) were treated with Agrobacterium tumefaciens strains C58C1/GV2260 carrying the plasmid p35SGUSINT and EHA101 harbouring the plasmid pIBGUS. In both vectors the GUS gene is interrupted by an intron. After inoculation shoot formation was promoted on MS medium containing 0.5 mg/l BAP under a selection pressure of 100 mg/l kanamycin or 10 mg/l phosphinothricin, depending on the construct used for transformation. Expression of the chimeric GUS gene was confirmed by histochemical localization of GUS activity in regenerated shoots. Resistant shoots were grafted onto 5-day-old dark-grown seedlings, and mature plants could be recovered. T-DNA integration was confirmed by Southern analysis by random selection of putative transformants. The analysis of 4 plantlets of the T1 progeny revealed that none of them was GUS-positive, whereas the presence of the nptII gene could be detected by polymerase chain reaction. Received: 30 May 1997 / Revision received: 18 September 1997 / Accepted: 22 March 1999     

Zeatin-induced shoot regeneration from immature chickpea (Cicer arietinum L.) cotyledons

For the purpose of developing an in vitro regeneration system for chickpea (Cicer arietinum L.), an important food legume, immature cotyledons approximately 5 mm long were excised from developing embryos and cultured on B5 basal medium supplemented with 1.5% sucrose and various growth regulator combinations. Only non-morphogenic callus was formed in response to concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D), naphthaleneacetic acid (NAA) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) previously reported to induce somatic embryogenesis on immature soybean cotyledons. However, 4.6, 13.7, and 45.6 M zeatin induced formation of white, cotyledon-like structures (CLS) at the proximal end of immature cotyledons placed with adaxial surface facing the agar medium. No morphogenesis, or occasional formation of fused, deformed CLS, was observed when zeatin was replaced with kinetin or 6-benzyladenine, respectively. The highest response frequency, 64% of explants forming CLS, was induced by 13.7 M zeatin plus 0.2 M indole-acetic acid (IAA). Within 20–40 days culture on zeatin, shoots formed at the base of CLS on approximately 50% of CLS-bearing explants, and proliferated upon subsequent transfer to basal medium with 4.4 M BA or 4.6 M kinetin. This regeneration system may be useful for genetic transformation of chickpea.     

Genetic analyses and conservation of QTL for ascochyta blight resistance in chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis> L.)

Ascochyta blight (AB) caused by Ascochyta rabiei (teleomorph, Didymella rabiei) Pass. Lab. is an important fungal disease of chickpea worldwide. Only moderate sources of resistance are available within the cultivated species and we hypothesized that the available sources may carry different genes for resistance, which could be pyramided to improve field resistance to AB. Four divergent moderately resistant cultivars CDC Frontier, CDC Luna, CDC Corinne, and Amit were each crossed to a highly susceptible germplasm ICCV 96029. Parents, F₁ and F₂ generations were evaluated under controlled conditions for their reactions to AB. A total of 144 simple sequence repeat (SSR) markers were first mapped to eight linkage groups (LG) for the CDC Frontier × ICCV 96029 population. Then based on the evidence from this population, 76, 61, and 42 SSR markers were systematically chosen and mapped in CDC Luna, CDC Corinne, and Amit populations, respectively. Frequency distributions of the AB rating in the F₂ generation varied among the four populations. Composite interval mapping revealed five QTLs (QTL1–5), one on each of LG 2, 3, 4, 6, and 8, respectively, distributed across different sources, controlling resistance to AB. CDC Frontier contained QTL2, 3, and 4 that simultaneously accounted for 56% of phenotypic variations. CDC Luna contained QTL 1 and 3. CDC Corinne contained QTL 3 and 5, while only QTL 2 was identified in Amit. Altogether these QTL explained 48, 38, and 14% of the estimated phenotypic variations in CDC Luna, CDC Corinne, and Amit populations, respectively. The results suggested that these QTLs could be combined into a single genotype to enhance field resistance to AB. Y. Anbessa and B. Taran contributed equally to this work.     

28-Homobrassinolide ameliorates the saline stress in chickpea (Cicer arietinum L.)

The response of chickpea (Cicer arietinum L.) cv. KPG-59 to pre-sowing seed treatment with 28-homobrassinolide (HBR) and/or sodium chloride (NaCl) was investigated. The seeds imbibed in aqueous solution of 10⁻¹⁰ or 10⁻⁸ M of HBR for 8 h, resulted in an increase in the values for most of the characteristics of shoot and root at 90-day stage and seed yield, at harvest. The plants resulting from the seeds soaked in HBR (10⁻⁸ M) possessed 23% and 31% higher leaf nitrate reductase (E.C. 1.6.6.1) and carbonic anhydrase (E.C. 4.2.2.1) activities, 34% more dry mass, 30% higher nodule number, 31% and 18% more nodule fresh and dry mass, compared with water soaked, control. Leghaemoglobin content and nitrogenase activity (E.C. 1.7.99.2) were 28% and 30% higher while nodule nitrogen and carbohydrate contents decreased by 5% and 6%, compared with the control. Moreover, seed yield increased by 26% over the control, at harvest. The values for all the above characteristics declined significantly, in the plants raised from the seeds soaked in NaCl. However, this ill effect was overcome, if NaCl treatment was given before or after HBR treatment.     

Osmotic adjustment as a mechanism of dehydration postponement in chickpea (Cicer arietinum L.) leaves

The objectives of this study were to test the existence of osmotic adjustment in a field-grown chickpea (Cicer arietinum L.) and to reproduce it in controlled conditions for a more complete study. In a first experiment, carried out in the field with the cultivar Casoar, we described two types of drought stress that a field-grown chickpea could experience during flowering in our conditions. They were characterized with soil and plant water status. Osmotic adjustment was taking place when the stress increased progressively. This evidence was obtained with the measurement of plant water potential and relative water content during a drying-rewatering cycle. In a second experiment, carried out in pots with rain shelter, with cultivars Casoar and Sombrero, we reproduced this particular type of drought stress, on the basis of soil water potential. Measurement of plant water status was based on water, osmotic, and turgor potentials, and relative water content. It showed that chickpea is able to realize osmotic adjustment during a controlled drying-rewatering cycle limited in intensity and duration. The analysis of a broad range of solutes (nitrate, sucrose, glucose, proline, malic acid and six other organic acids) gave a good explanation of the measured reduction of osmotic potential. Organic acids accounted for most of this reduction: 97% for Casoar and 96% for Sombrero. Malic acid, which represented about half of these acids, and malonic acid significantly accumulated during the drought stress. They explained 78.2% (for Casoar) and 75.8% (for Sombrero) of the reduction of osmotic potential. Cultivar Sombrero was the only one able to accumulate some sucrose.     

Paenibacillus lentimorbus enhances growth of chickpea (Cicer arietinum L.) in chromium-amended soil

Chromium (Cr), with its great economic importance in industrial use, is a major metal pollutant of the environment. It affects soil microbial activity and soil fertility, resulting in losses in yield of plants. Paenibacillus lentimorbus B-30488^r (B-30488^r) tolerated 200 μg ml⁻¹ of Cr under in vitro conditions and produced the plant growth promoting substance indole acetic acid in the presence of Cr. Our in vitro study indicates enhancement in B-30488^r biofilm formation by sodium alginate (SA) and calcium chloride (CaCl₂) both in absence and presence of supplemented Cr(VI) as compared to unsupplemented control. The plant growth promoting effects caused by the B-30488^r biofilm in rhizosphere of chickpea under Cr(VI) stress suggests a phytoprotective role of B-30488^r biofilm. Our study reflects the multifarious role of strain B-30488^r and presents it as a potent plant growth promoting and bioremediation agent useful in Cr-contaminated rhizosphere soil, whereby the SA and CaCl₂ induced B-30488^r biofilm on plant root acts as a shield in preventing the direct access of toxic Cr to plant tissues, thus reducing its uptake in plants.     

Effects of selection criteria on yield stability in chickpea (Cicer arietinum L.)

Summary Selection in the F₃ generation for seed yield, fruiting branches/plant, effective pods/plant, and seed index (100-seed weight) was carried out in two chickpea crosses. Sixty F₅ lines (15 lines/selection criterion) along with check variety were evaluated for seed yield in three distinct environments. The effects of selection criteria on yield stability was examined using linear regression approach and genotype-grouping technique. There were no differences between selection criteria for linear yield responses of F₅ lines to different environments. Within all four selection criteria the lines showed similar linear responses. The non-linear component was relatively higher for lines selected for effective pods and seed index than lines selected for yield and fruiting branches. On the basis of mean yield and coefficient of variation across environments, the seed index was the least effective selection criterion for developing high yielding and stable lines. When the results of stability parameters and genotype-grouping technique were considered together, selection for yield and fruiting branches was highly effective for isolating stable and high yielding lines.     

QTL analysis for ascochyta blight resistance in an intraspecific population of chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis> L.)

In both controlled environment and the field, six QTLs for ascochyta blight resistance were identified in three regions of the genome of an intraspecific population of chickpea using the IDS and AUDPC disease scoring systems. One QTL-region was detected from both environments, whereas the other two regions were detected from each environment. All the QTL-regions were significantly associated with ascochyta blight resistance using either of the disease scoring systems. The QTLs were verified by multiple interval mapping, and a two-QTL genetic model with considerable epistasis was established for both environments. The major QTLs generally showed additive gene action, as well as dominance inter-locus interaction in the multiple genetic model. All the QTLs were mapped near a RGA marker. The major QTLs were located on LG III, which was mapped with five different types of RGA markers. A CLRR-RGA marker and a STMS marker flanked QTL 6 for controlled environment resistance at 0.06 and 0.04 cM, respectively. Other STMS markers flanked QTL 1 for field resistance at a 5.6 cM interval. After validation, these flanking markers may be used in marker-assisted selection to breed for elite chickpea cultivars with durable resistance to ascochyta blight. The tight linkage of RGA markers to the major QTL on LG III will allow map-based cloning of the underlying resistance genes.Communicated by P. Langridge     

Early generation yield testing versus visual selection in chickpea (Cicer arietinum L.)

Summary Four F₃ populations of chickpea (Cicer arietinum L.) were simultaneously evaluated for yield in an F₃ yield trial and in single plant progeny rows. Ten high yielding, 10 low yielding and 10 randomly sampled lines, along with 10 lines visually selected for yield from the progeny rows, were retained for further evaluation. The lines from each of the four selection groups in each population were bulked and evaluated in a replicated yield trial at three locations and four environments. The bulk of visually selected lines was not superior in yield to the bulk of randomly sampled lines at all locations. The present results indicate that an early generation yield testing selection procedure is more efficient than visual selection for yield improvements in chickpea.     

Pathotype-specific genetic factors in chickpea (Cicer arietinum L.) for quantitative resistance to ascochyta blight

Ascochyta blight in chickpea (Cicer arietinum L.) is a devastating fungal disease caused by the necrotrophic pathogen, Ascochyta rabiei (Pass.) Lab. To elucidate the genetic mechanism of pathotype-dependent blight resistance in chickpea, F₇-derived recombinant inbred lines (RILs) from the intraspecific cross of PI 359075(1) (blight susceptible) × FLIP84-92C(2) (blight resistant) were inoculated with pathotypes I and II of A. rabiei. The pattern of blight resistance in the RIL population varied depending on the pathotype of A. rabiei. Using the same RIL population, an intraspecific genetic linkage map comprising 53 sequence-tagged microsatellite site markers was constructed. A quantitative trait locus (QTL) for resistance to pathotype II of A. rabiei and two QTLs for resistance to pathotype I were identified on linkage group (LG)4A and LG2+6, respectively. A putative single gene designated as Ar19 (or Ar21d) could explain the majority of quantitative resistance to pathotype I. Ar19 (or Ar21d) appeared to be required for resistance to both pathotypes of A. rabiei, and the additional QTL on LG4A conferred resistance to pathotype II of A. rabiei. Further molecular genetic approach is needed to identify individual qualitative blight resistance genes and their interaction for pathotype-dependent blight resistance in chickpea.     

Genetic variability and population structure of Mexican chickpea (Cicer arietinum L.) germplasm accessions revealed by microsatellite markers

Journal of Plant Biochemistry and Biotechnology - Globally, the chickpea is the second most important dried grain legume after bean. Mexico occupies eighth place as producer and fourth as exporter...     

QTL mapping of stalk bending strength in a recombinant inbred line maize population

Stalk bending strength (SBS) is a reliable indicator for evaluating stalk lodging resistance of maize plants. Based on biomechanical considerations, the maximum load exerted to breaking (F _max), the breaking moment (M _max) and critical stress (σ _max) are three important parameters to characterize SBS. We investigated the genetic architecture of SBS by phenotyping F _max, M _max and σ _max of the fourth internode of maize plants in a population of 216 recombinant inbred lines derived from the cross B73 × Ce03005 evaluated in four environments. Heritability of F _max, M _max and σ _max was 0.81, 0.79 and 0.75, respectively. F _max and σ _max were positively correlated with several other stalk characters. By using a linkage map with 129 SSR markers, we detected two, three and two quantitative trait loci (QTL) explaining 22.4, 26.1 and 17.2 % of the genotypic variance for F _max, M _max and σ _max, respectively. The QTL for F _max, M _max and σ _max located in adjacent bins 5.02 and 5.03 as well as in bin 10.04 for F _max were detected with high frequencies in cross-validation. As our QTL mapping results suggested a complex polygenic inheritance for SBS-related traits, we also evaluated the prediction accuracy of two genomic prediction methods (GBLUP and BayesB). In general, we found that both explained considerably higher proportions of the genetic variance than the values obtained in QTL mapping with cross-validation. Nevertheless, the identified QTL regions could be used as a starting point for fine mapping and gene cloning.