Identification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in arabica coffee

Resistance to Coffee Berry Disease (CBD) in Arabica coffee is controlled by at least three genes which are present in the varieties Hibrido de Timor (T gene), Catimor (T gene), Rume Sudan (R and k genes) and K7 (k gene). Hibrido de Timor, Catimor and Rume Sudan are genetically distant from most of the commercial cultivars, and the utilisation of molecular markers would greatly improve the efficiency of breeding programmes concerned with CBD resistance. The objectives of the present work were therefore: (1) to identify random amplified polymorphic DNA (RAPD) markers associated with CBD resistance and (2) to identify markers which could be used to select against the genetic background of the resistance donors. Identification of RAPD markers was carried out in three steps. The first step involved the comparison of the RAPD profiles between the susceptible cultivars and the resistant donors. This was followed by comparison of the RAPD profiles between resistant and susceptible types of each donor variety. The final step involved assay of the resistance markers in the first and the second backcrosses between these donors and the recurrent parent. High genetic variability was demonstrated in Catimor, and to some extent in Rume Sudan. Three RAPD markers were shown to be closely associated to the T gene. Attempts to identify markers associated with the R and k genes were less rewarding. The implications of the current observations in relation to breeding for CBD resistance in Arabica coffee are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Race-specificity and inheritance of incomplete resistance to coffee leaf rust in some Icatu coffee progenies and derivatives of Hibrido de Timor

Summary Selfed and cross-pollinated progenies of Icatu coffee plants and derivatives of Híbrido de Timor, with susceptibility or moderate resistance to coffee rust in the field, were tested with Hemileia vastatrix race II and isolate 2 (Is. 2) in the greenhouse or laboratory. Progenies from plants with a susceptible reaction type in the field (scores 8 and 9) all showed homogeneous levels of susceptibility similar to that of the control cultivars Mundo Novo and Catuaí of Coffea arabica. Variation for incomplete resistance was mainly expressed by low or heterogeneous reaction types and also by longer latency periods. Incomplete resistance to race II of some Icatu and Catimor plants, which is overcome by Is. 2, appeared to depend on a partially dominant gene. The expression of this gene may vary also according to the genetic background and some residual resistance to Is. 2 was observed. A few derivatives of Híbrido de Timor were more resistant to Is. 2 than to race II, suggesting the presence of a resistant factor to Is. 2 in this germplasm. Segregation in progenies from other plants with incomplete resistance to race II suggested presence of one or a few genes only, which in homozygous condition or in combination seem to confer near-complete or complete resistance. The results suggest that selection for incomplete resistance, expressed by intermediate reaction types, in Icatu and derivatives of Híbrido de Timor may not provide durable resistance to coffee rust. On the other hand, due to apparent additive gene action, phenotypic selection of plants with a highly resistant reaction type could facilitate the accumulation of several resistance alleles in one genotype, which could provide an efficient barrier against new race formation of the pathogen.     

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.     

Genetical analysis of resistance to Mycosphaerella pinodes in pea seedlings

Summary In studies of the inheritance of resistance, pea seedlings of seven lines in which stems and leaves were both resistant to Mycosphaerella pinodes were crossed with a line in which they were both susceptible. With seven of the crosses resistance was dominant to susceptibility. When F₂ progenies of five crosses were inoculated on either stems or leaves independently, phenotypes segregated in a ratio of 3 resistant: 1 susceptible indicating that a single dominant gene controlled resistance. F₂ progenies of one other cross gave ratios with a better fit to 9 resistant: 7 susceptible indicating that two co-dominant genes controlled resistance. The F₂ progeny of another cross segregated in complex ratios indicating multigene resistance.When resistant lines JI 97 and JI 1089 were crossed with a susceptible line and leaves and stems of each F₂ plant were inoculated, resistance phenotypes segregated independently demonstrating that leaf and stem resistance were controlled by different genes. In two experiments where the F₂ progeny of the cross JI 97×JI 1089 were tested for stem and leaf resistance separately, both characters segregated in a ratio of 15 resistant:1 susceptible indicating that these two resistant lines contain two non-allelic genes for stem resistance (designated Rmp1 and Rmp2) and two for leaf resistance (designated Rmp3 and Rmp4). Evidence that the gene for leaf resistance in JI 1089 is located in linkage group 4 of Pisum sativum is presented.     

Identification of alleles at two loci controlling resistance to Phomopsis stem blight in narrow-leafed lupin (Lupinus angustifolius L.)

The genetics of resistance to Phomopsis stem blight caused by Diaporthe toxica Will., Highet, Gams & Sivasith. in narrow-leafed lupin (Lupinus angustifolius L.) was studied in crosses between resistant cv. Merrit, very resistant breeding line 75A:258 and susceptible cv. Unicrop. A non-destructive glasshouse infection test was developed to assess resistance in the F₁, F₂, selected F₂-derived F₃ (F_2:3) families, and in selfed parent plants. The F₁ of Unicrop × 75A:258 (and reciprocal cross) was very resistant, and the F₂ segregated in a ratio of 3:1 (resistant: susceptible), which suggested the presence of a single dominant allele for resistance in 75A:258. In Merrit × Unicrop (and reciprocal), the F₁ was moderately resistant, and the F₂ segregated in a ratio of 3:1 (resistant: susceptible). Thus Merrit appeared to carry an incompletely dominant resistance allele for resistance. The F₁ of Merrit × 75A:258 (and reciprocal) was very resistant and the F₂ segregated in a ratio of 15:1 (resistant: susceptible), which supported the existence of independently segregating resistance alleles for resistance in 75A:258 and Merrit. Alleles at loci for early flowering (Ku) and speckled seeds (for which we propose the symbol Spk) segregated normally and independently of the resistance alleles. Resistant F₂ plants gave rise to uniformly resistant or segregating F_2:3 families, whereas susceptible F₂ plants gave rise only to susceptible F_2:3 families. However, the variation in resistance in the F₂ and some F_2:3 families of crosses involving 75A:258, from moderately to extremely resistant, was greater than that expected by chance or environmental variation. We propose the symbols Phr1 to describe the dominant resistance allele in 75A:258, and Phr2 for the incompletely dominant resistance allele in Merrit. Phr1 appears to be epistatic to Phr2, and expression of Phr1 may be altered by independently segregating modifier allele(s). This revised version was published online in July 2006 with corrections to the Cover Date.     

Inheritance of resistance to pea blight (Ascochyta pinodella) and induction of resistance in pea (Pisum sativum L.)

Summary Pea blight caused by Assochyta pinodella does considerable damage to the pea crop every year. To ascertain the inheritance of resistance to pea blight and incorporate resistance in the commercial cultivars, crosses were made between Kinnauri resistant to pea blight and four highly susceptible commercial pea cultivars — Bonneville, Lincoln, GC 141 and Sel. 18. Studies of the F₁'s, F₂'s, back crosses and F₃'s indicated that Kinnauri carries a dominant gene imparting resistance to pea blight.     

Inheritance of resistance to black rot (Xanthomonas campestris pv. Campestris) in cauliflower (Brassica oleracea var. Botrytis)

Summary Black rot disease caused by Xanthomonas campestris pv. campestris is a limiting factor in the commercial production of the cauliflower crop. Crosses were attempted between SN 445, a mid season cultivar resistant to black rot and two highly susceptible commercial cultivars (Pusa Snowball-1 and K-1). Studies of the F₁'s, F₂'s and back crosses indicated that SN 445, carries a dominant gene imparting resistance to black rot.     

Genetic analysis of partial resistance to coffee leaf rust ( Hemileia vastatrix Berk & Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species

The objective of this study was to identify polymorphic molecular markers associated with partial resistance to coffee leaf rust, Hemileia vastarix. A segregating F ₂ population derived from a cross between the susceptible Coffea arabica cv. Caturra and a C. canephora-introgressed Arabica line exhibiting high partial resistance was analyzed. Rust resistance measured as rust incidence (RI) and defoliation (DEF) was evaluated in field conditions in three consecutive years (2003–2005). During the 2003 season, which was characterized by favorable conditions for a rust epidemic, the F ₂ plants exhibited different levels of resistance ranging from very susceptible (50.1% for DEF and 49.5% for RI) to highly partial resistance (9.1% for DEF and 3.7% for RI). Molecular analysis enabled identification of seven polymorphic markers (5 AFLP and 2 SSR) exhibiting significant association with partial resistance. Coexistence of resistance homozygous alleles (RR) at codominant SSR loci was correlated with high resistance. This study is the first attempt to develop PCR-based sequence specific markers linked to partial rust resistance in coffee.     

Inheritance of coffee leaf rust resistance and identification of AFLP markers linked to the resistance gene

The most important disease of Coffea arabica is coffee leaf rust caused by the fungus Hemileia vastatrix. The purpose of this study was to characterize the inheritance of coffee resistance gene(s) to race II of this pathogen and to identify and map molecular markers linked to this trait. Different populations were used: F₂ (160 plants), BCr (20), and BCs (135), derived from a cross between the resistant genotype Híbrido de Timor UFV 427-15 and the susceptible cultivar Catuaí Amarelo UFV 2143-236 (IAC 30). The segregation analysis showed that the resistance of Híbrido de Timor to race II of the H. vastatrix is conferred by a single dominant gene. The amplification of 176 AFLP (Amplified fragment length polymorphism) primer combinations using bulked segregant analysis (BSA) allowed the identification of three molecular markers linked to the resistance gene. Genetic mapping of these three markers in the F₂ population indicated that they are distributed on both sides, flanking the resistance gene. The markers E.CTC/M.TTT405 and E.CGT/M.TGT300 were found linked to the resistance gene at 8.69 cM (LOD 18.91) and 25.10 cM (LOD 5.37), respectively, while E.CCT/M.TTC230 was localized on the other side of the gene, at 20.50 cM (LOD 6.15). These markers are the first rust resistance markers identified in Híbrido de Timor and can be useful for marker assisted selection in coffee breeding programs.     

Genetics of disease resistance in urdbean (Vigna mungo (L.) Hepper) to the leaf spots caused by Colletotrichum truncatum (Schw.) Andrus & Moore

Summary The resistance sources among various test cultivars of urdbean to Colletotrichum truncatum, a leaf spotting pathogen, were identified and genetics of resistance was worked out by studying F₁, F₂ and F₃ generations of crosses between resistant cultivars and the susceptible cv. Kulu 4 and of those among the resistant parents. The resistance was found to be controlled by single dominant genes and the resistance genes were non-allelic.     

Additional evidence for oligogenic inheritance of durable host resistance to coffee berry disease (<Emphasis Type="Italic">Colletotrichum kahawae</Emphasis>) in arabica coffee (<Emphasis Type="Italic">Coffea arabica</Emphasis> L.)

Breeding for host resistance to coffee berry disease (CBD) in arabica coffee (Coffea arabica) was initiated some 35–40 years ago in Kenya, Ethiopia and Tanzania in response to severe CBD epidemics. The release of CBD resistant cultivars to the coffee growers has been in progress since 1985. The resistance of cultivars like Ruiru 11 (Kenya) and Ababuna (and other cvs in Ethiopia) appears to be of a durable nature, since confirmed cases of a breakdown of host resistance under field conditions have not been reported over the past 20 years. Host resistance to the hemibiotrophic fungus Colletotrichum kahawae is of a quantitative nature, but nevertheless can be practically complete in some genotypes of arabica coffee. There is still no consensus on the genetics of CBD resistance, some claiming convincing evidence for oligogenes (1–3 major genes) and others for polygenes determining CBD resistance. Results from genetic studies with germplasm from the centre of genetic diversity for C. arabica in Ethiopia are presented here. These together with the recent identification of molecular markers associated with and the mapping of one major gene, provides additional evidence for oligogenic inheritance of CBD resistance. The development of cultivars combining yield and quality with durable host resistance to CBD has contributed greatly to increased sustainability of arabica coffee production in Africa. It has also considerable relevance to arabica coffee in Latin America and Asia, where CBD is still a quarantine disease but with a risk of becoming endemic one day, just as has happened earlier with coffee leaf rust (Hemileia vastatrix).     

Identification of a major QTL for adult plant resistance to coffee leaf rust (Hemileia vastatrix) in the natural Timor hybrid (Coffea arabica x C. canephora)

Most of the commercial varieties of coffee (Coffea arabica L.) derived from the Timor hybrid (TH) have been shown to contain major genes for coffee leaf rust (CLR) resistance. To identify markers tightly linked to such genes, an F₂ mapping population derived from a cross between ‘Caturra’ (susceptible variety) and the TH‐derived DI.200 line (highly resistant) was generated. Using expressed sequence information and a bioinformatics approach, both targeted region amplified polymorphism (TRAPs) markers and simple sequence repeat (SSR) markers were identified. Phenotypic evaluations in the field and under controlled conditions confirmed the existence of one quantitative trait locus for CLR resistance. Four candidate SSR markers were associated with high CLR resistance. They spanning a region of 2.5 cM designated Q_{CLR_4} located within chromosome 4 of the international C. canephora map. The presence of this region was confirmed in a set of elite lines and commercial varieties. The Q_{CLR_4} region corresponds to a new and genetically independent S_H locus that could potentially be useful in gene pyramiding with other genes to enhance rust resistance in TH derivatives.     

Effects of resistance genes,heat tolerance genes and cytoplasms on expression of resistance to Pseudomonas solanacearum (E.F. Smith) in potato

Summary Effects of resistance genes and heat tolerance genes on expression of resistance to bacterial wilt caused by Pseudomonas solanacearum were investigated in 30 F₁ progenies from parents with different levels of bacterial wilt resistance and heat tolerance. A race 1 and a race 3 isolate of the bacterium were used for inoculation under screenhouse conditions at two locations. Results obtained indicated that with reduction in levels of parental resistance, resistance in the F₁ progenies was also reduced. Under hot conditions, a reduced heat tolerance in the genetic background also resulted in lower levels of resistance expression. The effect of heat tolerance tended to diminish at lower temperatures leaving the effect of resistance genes more consistent. There existed a strong interaction between resistance genes and genes for heat tolerance. The nature of resistance to bacterial wilt in potato and implications for breeding for resistance are discussed.Effects of reciprocal crosses on expression of resistance to a race 1 isolate under hot screenhouse conditions, were studied in 5 sets of reciprocal F₁ progenies involving different resistant and susceptible parents. The reciprocal differences observed were not significant suggesting absence of cytoplasmic effects on expression of resistance.     

Inheritance of resistance to angular leaf spot in Nicotiana tabacum L. cultivars burley 21 and kentucky 14

Summary The genetics of resistance to angular leaf spot caused by Pseudomonas syringae pv. tabaci in Nicotiana tabacum cultivars Burley 21 and Kentucky 14 was investigated by studying disease reactions to three isolates of parental, F₁, F₂ and backcross generations derived from crosses between the resistant cultivars and the susceptible cultivar Judy's Pride. Studies were conducted in the greenhouse and in field plant beds. Chi-square values were computed to determine whether the observed ratios for disease reactions deviated from expected Mendelian ratios for a single, dominant gene controlling resistance to angular leaf spot in tobacco. Based on the resistance of the F₁ and the backcross generation to the resistant parent (BC-R), a 3 resistant: 1 susceptible segregation ratio in the F₂, and a 1 resistant: 1 susceptible segregation ratio in the backcross generation to the susceptible parent (BC-S), it was concluded that resistance to three isolates of Pseudomonas syringae pv. tabaci is governed by a single, dominant gene.     

Inheritance of resistance to angular leaf spot (Isariopsis griseola Sacc.) in french bean (Phaseolus vulgaris L.)

Summary Angular leaf spot (Isariopsis griseola Sacc.) is a serious disease of French bean in the hills of India and 40 to 70 per cent of the green pods are damaged and rendered unmarketable. Crosses were made between PLB 257, (Phaseolus coccineus L.), a red flowering pole tope, resistant to angular leaf spot, and Contender (Phaseolus vulgaris L.), a highly susceptible commercial cultivar. Studies of the F₁, F₂, and F₃ progenies indicated that PLB 257, carries a recessive gene imparting resistance to angular leaf spot.     

Inheritance of partial resistance to Myzus persicae in lettuce

Summary The genetics of partial resistance of lettuce to Myzus persicae was studied using F₁ and F₂ generations of two crosses between a susceptible and partially resistant accession (Norden x Batacer and Liba x Norden) and three crosses in which both parents were partially resistant (Batavia la Brillante x Batacer, Batacer x Liba and CGN4741 x Batacer). Partial resistance to M. persicae inherited quantitatively, without important dominance effects. Only in the cross Batacer x Liba were significant departures of the F₁ and F₂ from the midparent found, which were probably caused by epistatic effects. Reciprocal F₁s had similar resistance levels, indicating the absence of cytoplasmic or other maternal effects. Estimates of broad-sense heritability ranged from 0.34 to 0.61. The results indicated that lines with an improved resistance level can be obtained from crosses between partially resistant accessions, preferably by line selection or the application of indirect marker aided selection.Abbreviations PR partial resistance, partially resistant - S susceptibility, susceptible     

Inheritance of anthracnose resistance in the common bean cultivar Widusa

Snap bean (Phaseolus vulgaris L.) cultivar, Widusa, was crossed to Michigan Dark Red Kidney (MDRK), Michelite, BAT 93, Mexico 222, Cornell 49–242, and TO cultivars to study the inheritance of resistance to anthracnose in Widusa. The segregation patterns observed in six F₂ populations supported an expected 3R:1S ratio suggesting that Widusa carries a single dominant gene conditioning resistance to races 7, 65, 73, and 453 of Colletotrichum lindemuthianum, the causal organism of bean anthracnose. Allelism tests conducted with F₂ populations derived from crosses between Widusa and Cornell 49–242 (Co-2), Mexico 222 (Co-3), TO (Co-4), TU (Co-5), AB 136 (Co-6), BAT 93 (Co-9), and Ouro Negro (Co-10), inoculated with races 7, 9, 65 and 73, showed a segregation ratio of 15R:1S. These results suggest that the anthracnose resistance gene in Widusa is independent from the Co-2, Co-3, Co-4,Co-5, Co-6, Co-9, and Co-10 genes. A lack of segregation was observed among 200 F₂ individuals from the cross Widusa/MDRK, and among 138 F₂ individuals from the cross Widusa/Kaboon inoculated with race 65, suggesting that Widusa carries an allele at the Co-1 locus. We propose that the anthracnose resistance allele in Widusa be named Co-1 ⁵ as Widusa exhibits a unique reaction to race 89 compared to other alleles at the Co-1 locus. RAPD marker A18₁₅₀₀ co-segregated in repulsion-phase linkage with the Co-1 ⁵ gene at a distance of 1.2 cM and will provide bean breeders with a ready tool to enhance the use of the Co-1 ⁵ gene in future bean cultivars.     

A novel source of resistance to the two-spotted spider mite in Lycopersicon pimpinellifolium (Jusl.) Mill.: its genetics as affected by interplot interference

We have previously found an accession of Lycopersicon pimpinellifolium (Jusl.) Mill. (`TO-937') that appeared to resist attack by the two-spotted spider mite (Tetranychus urticae Koch). L. pimpinellifolium is a very close relative of the cultivated tomato (Lycopersicon esculentum Mill.) and thereby a potential source of desirable traits that could be introgressed to the crop species. The objective of this study was to investigate the genetics of the resistance present in `TO-937'. Resistance to infestation by the spider mite was quantified in 24-plant plots of L. pimpinellifolium accessions `TO-937' and `PE-10', L. pennellii accession `PE-45', L. esculentum cultivars `Moneymaker', `Roma' and `Kalohi' (reported to be partially resistant: Stoner & Stringfellow, 1967), and the interspecific F₁ cross, L. esculentum `Moneymaker' × L. pimpinellifolium `TO-937'. Only `TO-937', the F<sub>1</sub>, and`PE-45' were found to be resistant. Resistance of `TO-937' was complete when evaluated in two small greenhouses completely planted with `TO-937' so as to simulate the genotypic homogeneity usual in commercial crops. Generations (P₁, P₂, F₁, F₂, BC₁P₁, and BC₁P₂) of a P₁ (susceptible) × P₂ (resistant) cross (`Moneymaker' × `TO-937') were studied for resistance in a single-plant per plot design. Resistance of `TO-937' was inherited with complete dominance and appeared to be controlled by either two or four genes according to whether segregation in the F₂ or the BC₁P₁, respectively, were considered. However, calculation of the number of genes involved in the resistance was complicated by negative interplot interference due to the high frequency of resistant genotypes within most of the generations. This revised version was published online in July 2006 with corrections to the Cover Date.     

Monogenic resistance in tomato to Fusarium oxysporum f. sp. lycopersici race 3

Summary Resistance to fusarium wilt, incited by Fusarium oxysporum (Schlecht.) f. sp. lycopersici (Sacc.) Snyder & Hansen race 3 in tomato (Lycopersicon esculentum Mill.) was discovered in LA 716, a L. pennellii accession. A resistant BC₁F₃ breeding line, E427, was developed from LA 716. E427 was crossed with the susceptible cv. Suncoast and F₁, BCP₁, BCP₂ (to Fla 7155, a susceptible parent) F₂, F₃, and BCP₂S₁ seeds were obtained. Segregation for resistance following root dip inoculation over three experiments indicated a single dominant gene controlled resistance. Five of the 12 BCP₁S₁'s segregated more susceptible plants, whereas one of the 12 segregated more resistant plants than expected (P<0.05). Three of 23 F₃ lines segregated more susceptible plants than expected while 1 of the 23 had more resistant plants than expected (P<0.05). Segregation in all other lines fit expected ratios. Five of the 23 F₃'s were homozygous resistant which was an acceptable fit to expectations (P=0.1–0.5). The gene symbol I ₃ is proposed for resistance to race 3 of the wilt pathogen. Deviations from expected ratios in data reported here and for other breeding lines indicate an effect of modifier genes and/or incomplete penetrance. Plant age at inoculation and seed dormancy did not affect results.Florida Agricultural Experiment Station Journal Series No. 8101.     

Inheritance of resistance to fruit rot (Phytophthora capsici Leon.) and induction of resistance in bell pepper (Capsicum annuum L.)

Summary Fruit rot in bell pepper caused by Phytopthora capsici Leon. is a limiting factor in its commercial production. Crosses were made between Waxy Globe, a small fruited hot type, resistant to fruit rot and four highly susceptible bell pepper commercial cultivars (Chinese Giant, California Wonder, Osh, Kosh and Yolo Wonder). Studies of the F₁'s, F₂'s and backcrosses indicated that Waxy Globe carries a dominant gene imparting resistance to fruit rot. After three backcrosses with California Wonder, lines were obtained combining the resistance gene of Waxy Globe with the large fruit size and low capsaicin of California Wonder.