Quantitative trait analysis in Theobroma cacao using molecular markers

The aim of this study was to determine the genetic components controlling yield in an F₁ cacao cross between Catongo and Pound 12 clones. Genetic maps were constructed for the two parents using molecular markers which detected 158 polymorphic loci covering 772 cM for the heterozygous genotype Pound 12 and only 4 loci representing 16.9 cM of a linkage group which indicated a high level of homozygosity of Catongo. Yield was recorded twice a month during 15 years on 55 individuals from this segregating population. Ten yield QTL were detected on eight linkage groups. Some of these QTL were frequently detected over 15 years of production, while others were specific for a given year. Total yield genetic variance, on a yearly basis, ranged from 0 to 56%. Two major QTL (E and I) each explained approximately 20% of the total variance of the average yield over 15 years. The analysis of potential cacao yield components, such as pod index and trunk diameter, suggested that some regions of the genome exert effects on more than one trait, providing a possible genetic explanation for the correlations detected between some of title traits studied. Data showed that correlation between successive annual yield decreased when the lag between corresponding seasons increased. When separated by more than 10 years, annual yields were no longer correlated. The utilisation of molecular markers alone or in combination with phenotypic selection showed an advantage in the early selection of the best cacao producer trees. Further use of molecular markers in breeding programs is discussed with a view to reducing the generation time of a selection procedure. This revised version was published online in July 2006 with corrections to the Cover Date.     

A study of genotype-isolate interaction in cacao (Theobroma cacao L.): resistance of cacao genotypes to isolates of Phytophthora palmivora

The resistance of cacao (Theobroma cacao. L)leaves to 10 isolates of Phytophthora palmivora(Butler) Butler was investigated in 18 genotypes of cacao in three experiments. Tissue-paper-mount and punch-inoculation methods were used to distinguish between resistance at the penetration and post-penetration levels based on lesion frequency and size, respectively. There was a 5–6 fold difference in aggressiveness among isolates collected from different locations in the islands of Trinidad and Tobago for both types of resistance. However, host genotype ×isolate interaction effects were not significant for resistance at both the penetration and post-penetration levels. A strong positive relationship (r = 0.8) was observed in the abilities of isolates to effectively breach the two types of resistance. This suggests that the same isolate can be used in screening for both types of resistance. No significant relationship was found between resistance at the penetration and post-penetration levels suggesting that the resistance mechanisms were different. Subsequent experiments using a wider range of cacao genotypes from the International Germplasm Collection, Trinidad, confirmed the initial results. These experiments indicate that resistance found using one isolate would be equally valid using other isolates of Phytophthora palmivora. The implications of the findings are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of adult-plant resistance to Phytophthora capsici in pepper

Summary Inheritance studies were conducted to determine the genetic basis of adult-plant resistance in pepper (Capsicum annuum L.) to Phytophthora capsici. F₁, backcrosses and F₂ populations were developed using the resistant parent Criollo de Morellos 334 and susceptible parents Agronômico 10-G and Yolo Wonder. Pepper plants, at 36 days post-emergence, were inoculated near the base of the stem with an inoculum suspension of 5×10⁴ zoospores/ml. Segregation ratios in the F₂ generation of 13 resistant to 3 susceptible plants fit a 2-gene model for resistance with dominant and recessive epistasis.     

Inheritance of resistance to Phytophthora fragariae Hickman in strawberry

Summary It has been found that complete resistance of the strawberry cultivars and selections Earliglow, Guardian, MdUS 2700, MdUS 2929, MdUS 3816 and Redchief to Phytophthora fragariae is inherited in a one-to-one ratio, suggesting that these genotypes have one major resistance gene effective to the races present in the test field.The high level of partial resistance of Cambridge Favourite has clearly been recovered in its progenies. However, from results presented here, no conclusions could be drawn with regard to the number of genes involved in the partial resistance of Cambridge Favourite. It is, however, suggestive that about half the susceptible selections derived from crosses with Cambridge Favourite have shown a relatively high level of partial resistance. The selections concerned were obtained by selection on horticultural characters in seedling populations planted on an uninfested field.     

Validity of a leaf inoculation test to assess the resistance to Phytophthora megakarya in a cocoa (Theobroma cacao L.) diallel mating design

Cocoa pod rot, caused by different Phytophthora species, is rife in all production zones. Phytophthora spp. control is therefore a major challenge for world cocoa cultivation, and selection of resistant material is a priority research theme for many producing countries. Various genetic trials have been set up over many years in zones affected by the disease. In Cameroon, a 6x6 diallel mating design was set up to study heritability of the resistance trait. Field observations led to the classification of parents according to their ability to transmit resistance to their progenies. These field measurements were long and laborious, so a resistance test based on artificial leaf inoculations was developed. This article studies the correspondence between results obtained with the test and observations of rot rates in the field. There was a significant genetic correlation between pod rot rate in the field and leaf test data, so using this resistance test could shorten cocoa tree selection cycles. This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of foliar resistance to Phytophthora palmivora (butler) Butler in cacao (theobroma cacao L.)

The genetic nature of resistance in leaves of cacao (Theobroma cacao L.) to Phytophthora palmivora (Butler) Butler was investigated in a 3 × 8 and a 4 × 4 mating design. Leaf resistance was assessed at the penetration and post-penetration stages of infection. Wide variability was observed among the 32 families examined for lesion frequency (penetration resistance) and lesion size / spread (post-penetration resistance). Segregation within families showed a continuous distribution for both forms of resistance, suggesting that resistance is polygenic. The poor association between resistance at the penetration stage and that at the post-penetration stage suggested that they were independently inherited and could be selected independently with the aim of accumulating genes for resistance. Genetic complementation between the two forms of resistance and transgressive segregation were evident within the families studied. The additive effects were predominant for lesion size, while both additive and non-additive effects were important in the inheritance of lesion frequency. The narrow sense heritabilities obtained from North Carolina Model II analysis were as high as 0.61 and 0.40 for lesion size and lesion frequency respectively. Possible breeding strategies based on these findings are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of resistance to late blight (Phytophthora infestans) in potato

Under epiphytotic conditions for late blight in spring seasons, data were recorded on its intensity four times at 4 days intervals from the start of the disease in the field, in 114 (19 females × 6 males) progenies and their parents planted in randomized complete block design in the years 2005 and 2006. Regression and stepwise regression analysis showed that observations during the rapidly increasing phase of disease between initial and last phase of disease are more important than the observations at initial and last phase of the disease. Combining ability analysis on a sub-set of 68 progenies showed that the additive component of genetic variance was more important than the non-additive component of variance in inheritance of quantitative resistance to late blight. The per se performance of the parents does give an idea about their general combining ability (GCA). However, selection of parents based on their GCA will be very useful for breeding for quantitative resistance to late blight. Parents JX 90, JF 4841, CP 3356, CP 1358, CP 3290, JN 1197 and CP 3125 were found to have good GCA for quantitative resistance for late blight and the best six crosses for late bilght resistance based on mean performance involved parents with good combining ability only.     

Molecular mapping of quantitative trait loci determining resistance to septoria tritici blotch caused by Mycosphaerella graminicola in wheat

A set of 65 recombinant inbred lines of the ‘International Triticeae Mapping Initiative’ mapping population (‘W7984’בOpata 85’) was analysed for resistance to septoria tritici blotch at the seedling and adult plant stages. The mapping population was inoculated with two Argentinean isolates (IPO 92067 and IPO 93014). At the seedling stage, three loci were discovered on the short arms of chromosomes 1D, 2D and 6B. All three loci were detected with both isolates. At the adult plant stage, two isolate-specific QTL were found. The loci specific for isolates IPO 92067 and IPO 93014 were mapped on the long arms of chromosomes 3D and 7B, respectively. This revised version was published online in August 2006 with corrections to the Cover Date.     

Inheritance and general combining ability studies of detached pod, leaf disc and natural field resistance to Phytophthora palmivora and Phytophthora megakarya in cacao (Theobroma cacao L.)

Black pod is a major disease of cocoa. Knowledge of the inheritance of resistance to black pod would be important in devising strategies to breed resistant varieties. The mode of inheritance of resistance to black pod disease was investigated using leaf disc, detached pod tests and natural field observation in a 6?×?4 factorial and 6?×?6 diallel mating designs analyzed using North Carolina design-II approach and Griffing??s method II model I approach, respectively. The dominant component was smaller than the additive component for pod lesion size, leaf disc scores and natural field infection. Both general combining ability and specific combining ability (SCA) effects influenced the inheritance of pod lesion number and leaf disc scores suggesting that both additive and non-additive (dominance or epistatic) effects influence the inheritance of resistance to black pod disease. However, SCA effect was not significant for pod lesion size and natural field infection suggesting the importance of additive genes in the inheritance of these traits. The higher heritability of leaf disc scores, pod lesion numbers and pod lesion sizes than the heritability of natural field infection which was almost zero, shows the influence of environment on natural field infection and suggests that ranking of resistance of cocoa genotypes need to be done under controlled environmental conditions to observe true resistance levels. Good general combiners, in combination with each other, did not necessarily yield good specific combinations suggesting that parents?? performance cannot be used for selecting superior progenies. The non-significance of reciprocal effects indicates absence of maternal effects or cytoplasmic inheritance in resistance to black pod disease. Recurrent selection procedures and inter-crossing aimed at general combining ability would be more suitable for improvement of black pod disease resistance. Cocoa genotypes with good combining ability for resistance to black pod disease such as T60/887, Pa 150, Sca 6, and Pa7/808, identified in this study could be important parents to form base population for such recurrent selection procedures.     

A quantitative trait locus influencing tolerance to Phytophthora root rot in the soybean cultivar ‘Conrad’

‘Conrad’, a soybean cultivar tolerant to Phytophthora root rot (PRR), and ‘OX760-6-1’, a breeding line with low tolerance to PRR, were crossed. F₂ derived recombinant inbred lines were advanced to F₆ to generate a population through single-seed descent. This population was used to identify quantitative trait loci (QTLs) influencing PRR tolerance in ‘Conrad’. A total of 99 simple sequence repeat (SSR), or microsatellite, markers that were polymorphic and clearly segregated in the F₆ mapping population were used for QTL detection. Based on the data of PRR in the field at two planting locations, Woodslee and Weaver, for the years 2000 and 2001, one putative QTL, designated as Qsatt414-596, was detected using MapMaker/QTL. Qsatt414-596 was flanked by two SSR markers from the linkage group MLG J, Satt414 and Satt596. Satt414 and Satt596 were also detected to be significantly (P < 0.005) associated with PRR using the SAS GLM procedure and were estimated to explain 13.7% and 21.5% of the total phenotypic variance, respectively.     

Association of RFLP markers with trait loci affecting clubroot resistance and morphological characters in Brassica oleracea L.

Summary Resistance to Plasmodiophora brassicae Wor. race 7, the causal agent of the disease clubroot, was examined in an F₂ population of a cross between a clubroot resistant broccoli (Brassica oleracea var. italica) and a susceptible cauliflower (B. oleracea var. botrytis). A genetic linkage map was constructed in the same population based on the segregation of 58 dispersed restriction fragment length polymorphism (RFLP) markers. Associations between the inheritance of RFLP marker genotypes and segregation for disease resistance, morphological and maturity characteristics were examined. For each triat examined, several chromosomal regions marked by RFLP probes appeared to contain trait loci, suggesting that each trait was under polygenic control. RFLP marker linkage to a major factor imparting dominance for clubroot resistance from the broccoli parent was observed in this population. Additionally, RFLP marker linkage to an independently segregating factor contributing clubroot resistance from the cauliflower parent was observed, indicating that it should be possible to use RFLP markers to facilitate selection of transgressive segregants having the combined resistance from both parental sources. In some instances, RFLP markers from the same or closely linked chromosomal regions were associated with both clubroot resistance and morphological traits. Analysis of RFLP marker genotypes at linked loci should facilitate the selection of desired disease resistant morphotypes.     

Quantitative trait loci mapping and epistatic analysis for grain yield and yield components using molecular markers with an elite maize hybrid

Summary The aim of this investigation was to map quantitative trait loci (QTL) associated with grain yield and yield components in maize and to analyze the role of epistasis in controlling these traits. An F_2:3 population from an elite hybrid (Zong3 × 87-1) was used to evaluate grain yield and yield components in two locations (Wuhan and Xiangfan, China) using a randomized complete-block design. The mapping population included 266 F_2:3 family lines. A genetic linkage map containing 150 simple sequence repeats and 24 restriction fragment length polymorphism markers was constructed, spanning a total of 2531.6 cM with an average interval of 14.5 cM. A logarithm-of-odds threshold of 2.8 was used as the criterion to confirm the presence of one QTL after 1000 permutations. Twenty-nine QTL were detected for four yield traits, with 11 of them detected simultaneously in both locations. Single QTL contribution to phenotypic variations ranged from 3.7% to 16.8%. Additive, partial dominance, dominance, and overdominance effects were all identified for investigated traits. A greater proportion of overdominance effects was always observed for traits that exhibited higher levels of heterosis. At the P ≤ 0.005 level with 1000 random permutations, 175 and 315 significant digenic interactions were detected in two locations for four yield traits using all possible locus pairs of molecular markers. Twenty-four significant digenic interactions were simultaneously detected for four yield traits at both locations. All three possible digenic interaction types were observed for investigated traits. Each of the interactions accounted for only a small proportion of the phenotypic variation, with an average of 4.0% for single interaction. Most interactions (74.9%) occurred among marker loci, in which significant effects were not detected by single-locus analysis. Some QTL (52.2%) detected by single-locus analysis were involved in epistatic interactions. These results demonstrate that digenic interactions at the two-locus level might play an important role in the genetic basis of maize heterosis.     

Quantitative trait loci of frost tolerance and physiologically related trait in faba bean (Vicia faba L.)

In faba bean, field based winter-hardiness is a complex trait that is significantly correlated to frost tolerance. Frost tolerance could be used to indirectly select for faba bean winter-hardiness. The aim of this study was to identify putative QTL associated with frost tolerance and auxiliary traits and to quantify the efficiency of marker assisted selection. Thus, 101 recombinant inbred lines derived from the cross between two frost tolerant lines were tested for their hardened and unhardened frost tolerance and for their leaf fatty acid content in both treatments. Significant differences among the RIL were observed for all studied traits. For frost tolerance, five putative QTL were detected; three for unhardened frost tolerance that explained 40.7% (8.6% after cross-validation, CV) of its genotypic variance and two for hardened frost tolerance that explained 21.8% (1.0% after CV). For fatty acid content, three QTL were detected for oleic acid content in unhardened leaves that explained 62.9% (40.6% after CV) of its genotypic variance. This fatty acid was significantly correlated with unhardened frost tolerance. The unbiased genotypic variance explained enabled to draw realistic prospects of MAS for frost tolerance. In this study, combined MAS was more efficient than classical phenotypic selection and was expected to be higher on larger populations at early generations. Moreover, favourable alleles inherited from the exotic line BPL 4628 could be introgressed to European winter-hardy beans for further improvement.     

Quantitative trait loci analysis of soluble sugar contents in soybean

The soluble sugar content in soybean seeds, mainly sucrose, stachyose, raffinose and trace amounts of glucose and fructose, is important for the increasing global market demand for various soyfoods including tofu, soymilk, natto, bean sprouts and edamame due to their nutritional value and health benefits. The objective of this study was to conduct quantitative trait loci (QTL) analysis and identify molecular markers for soluble sugar content in soybean seeds for marker‐assisted selection (MAS) in soybean breeding. The content of the five previously mentioned sugars were measured and associated QTLs were mapped based on a F₂ population that was derived from a cross between V97‐3000 and V99‐5089. Eleven QTLs were detected for the five sugar contents: one for glucose, three each for fructose and sucrose, and two each for raffinose and stachyose. However, only one QTL for sucrose, one QTL for raffinose, and two QTLs for stachyose were identified with LOD > 3.0 and R² > 10% from this research. The QTL on chromosome 11 [linkage group (LG) B1] was identified as associated with sucrose, raffinose and stachyose in the same region as previously reported for sucrose and stachyose. The SSR marker, Satt359, on the QTL B1 region had an significant association with sucrose (LOD = 5.192; R² = 0.134), raffinose (LOD = 3.95; R² = 0.104), and stachyose (LOD = 13.572; R² = 0.314); therefore it can be used to assist breeding selection for sucrose, raffinose and stachyose contents simultaneously.     

Inheritance of resistance to fruit rot (Phytophthora parasiticaDast.) in tomato (Lycopersicon esculentum Mill.)

Summary Fruit rot disease caused by Phytophthora parasiticaDast. is a limiting factor in tomato production in Himachal Pradesh. 30 to 60 per cent fruits are damaged by this disease. Crosses were made between EC 54725 (Lycopersicon pimpinellifolium), a small tyuited type, resistant to fruit rot and four highly susceptible tomato commercial cultivars (Gola, Sioux, S12, and Lalmani). Studies of F₁'s, F₂'s and back crosses indicated that EC 54725 carries a dominant gene imparting resistance to fruit rot.     

The genetic structure of cocoa populations (Theobroma cacao. L.) revealed by RFLP analysis

The genetic structure of 175 genotypes of Theobroma cacao L. was investigated using 27 RFLP/cDNA loci. The number of alleles per locus was never higher than four and a high genetic diversity was found. Criollo genotypes appeared differentiated from Forastero genotypes. A deficiency of heterozygotes was found in all populations and some alleles were fixed in some populations. Within population gene diversity was high. When four morphological groups were considered, Upper Amazon Forastero was the most polymorphic and diverse population. Almost all the alleles of the whole species could be found within this group. Observed heterozygosity was the highest within Criollo and Trinitario populations but a certain proportion of homozygous genotypes was present in all groups. This revised version was published online in July 2006 with corrections to the Cover Date.     

Evaluation and utilisation of cacao (Theobroma cacao L.) germplasm at the International Cocoa Genebank, Trinidad

The aim of this study was to identify promising genotypes in the International Cocoa Gene bank, Trinidad (ICG,T) for use in cacao breeding. Subsets of the germ plasm collection were evaluated for bean number, bean weight, pod index (581 genotypes) and resistance to Phytophthora pod rot(500 genotypes). Among three groups of cacao assessed (For astero, Refractario and Trinitario), Trinitario had the highest percentage of genotypes (36.9%) with large bean weight (> 1.2 g), while For astero possessed the highest proportion of genotypes (22.6%) with a large number of beans (> 45). The ICS population had the highest percentage (44.1%) of genotypes with heavy beans, and IMC the highest percentage of genotypes with large bean number (68.6%). A low, but significant negative correlation (r = –0.19, p≤ 0.001) between bean number and bean weight suggests that an increase in bean number may repress an increase in bean weight and vice versa. However, inten genotypes good values of bean weight and number were combined demonstrating that selection for both large bean number and bean weight is possible. The highest percentage (28.1%) of genotypes with low pod index (< 20.1) was observed in the Trinitario group (mainly ICS). The Forastero group had the highest percentage of Phytophthora resistant accessions(18.0%). The PA population had the highest proportion of resistant (24.0%) and moderately resistant (38.0%)genotypes. Sixty-five and 99 genotypes were categorised with large bean weight and high bean number, respectively, and 60 genotypes were found with a low pod index. Seventy-eight genotypes were identified with resistance to Phytophthora podrot. A significant relationship was observed between resistance to Phytophthora pod rot (measured as the frequency of localised lesions) and bean number (r = –0.45, p ≤ 0.001)showing that the two traits may complement each other. The combination of low to intermediate pod index with moderate to high resistance to Phytophthora podrot was found in 87 genotypes, 12 of which were also reported to have resistance to witches’ broom disease. These genotypes are of high potential value in cacao breeding and their inclusion in working and corecollections would be justified. This revised version was published online in July 2006 with corrections to the Cover Date.     

Quantitative trait loci analysis for resistance against Turnip mosaic virus based on a doubled-haploid population in Chinese cabbage

Turnip mosaic virus (TuMV) as the major virus infecting Brassica crops, often cause severe yield and quality losses in Chinese cabbage production in China. In this study, quantitative trait loci (QTL) analysis for TuMV resistance was conducted with a population of 100 doubled-haploid lines derived from the F₁ between 91-112 (resistant) and T12-19 (susceptible) through microspore culture. A total of 376 molecular markers including 235 amplified fragment length polymorphisms, 129 random amplified polymorphic DNAs, 10 simple sequence repeats, one SCAR and one morphological marker were employed to construct a linkage map with 10 linkage groups covering 809.1 cM with an average distance of 2.2 cM between loci. Resistance was assessed by artificial inoculation at the seedling stage and at the adult stage in field conditions, respectively. Four QTLs controlling TuMV resistance were identified with JoinMap QTL 4.0 and interval mapping method. Two QTLs ( Tu1 , Tu2 ) were associated with resistance at the seedling stage, each accounting for 58.2% and 14.7% of the phenotypic variation, respectively. Two QTLs ( Tu3 , Tu4 ) were found corresponding to the disease resistance at the adult plant stage, explaining 48.5% and 32.0% of the phenotypic variation, respectively. Marker-assisted selection for these major QTLs involved in TuMV resistance could be useful in Chinese-cabbage breeding programmes.     

Quantitative trait loci with additive and epistatic effects underlying resistance to two HG types of soybean cyst nematode

The resistance of soybean (Glycine max L. Merr.) cultivars varies with the different races of the soybean cyst nematode (SCN), Heterodera glycines, referred to as HG types (biotypes). Resistant cultivars with durable resistance are emphasized in recent years. The aim here was to identify quantitative trait loci (QTLs) for resistance to two SCN HG types (HG type 2.5.7, race 1; and HG type 1.2.3.5.7, race 4) in resistant cultivar ‘L‐10’ and to analyse the additive and epistatic effects of the identified QTLs. A total of 140 F₅‐derived F₁₀ recombinant inbred lines (F_5:10 RILs) were advanced via single‐seed‐descent from the cross between ‘L‐10’ (broadly resistant to SCN) and “Heinong 37” (SCN‐susceptible). For SCN HG type 2.5.7 and HG type 1.2.3.5.7 resistance, three and six QTLs for resistance to SCN HG type 2.5.7 and HG type 1.2.3.5.7 were identified, respectively, most of which could explain <10% of the phenotypic variation. Among these QTLs, five were identified over 2 years, while the other QTLs were detected in either 2009 or 2010. QSCN1‐2, located near the SSR marker Sat_069 of linkage group D1b (Chromosome, 2), was responsible for the largest proportion of phenotypic variation (16.01% in 2009 and 18.94% in 2010), suggested that it could effectively be used as a candidate QTL for the marker‐assisted selection (MAS) of soybean lines resistant to SCN. Additionally, for SCN HG type 2.5.7 and HG type 1.2.3.5.7 resistance, two and four QTLs showed an additive effect (a), respectively. One epistatic pair of QTLs (QSCN1‐1‐QSCN1‐3) for SCN HG type 2.5.7 resistance and eight epistatic pairs of QTLs for SCN HG type 1.2.3.5.7 resistance were found to have significant aa effects, among which one pair of QTLs (QSCN4‐4 and QSCN4‐5) contributed a large proportion of aa effects (3%). The results indicated that additive and epistatic effects could significantly affect SCN resistance. Therefore, both of a and aa effects should be considered in MAS programmes.