Selection for Resistance to Coffee Berry Disease, High Yields and Good Quality within Coffea arabica L. Cultivar, Ruiru 11

Abstract

Coffea arabica cv. Ruiru 11 is a composite of sixty six (66) F1 hybrid sibs each derived from a cross between a specific female and male population. The pedigree of Ruiru 11 consist of CBD resistance donors, Rume Sudan (R gene), Hibrido De Timor (T or Ck-1 gene), Catimor (T or Ck-1 gene), K7 (k gene), SL4 and the high yielding, good quality but susceptible cultivars such as N39, SL28, SL34 and Bourbon. Although the composite cultivar, Ruiru 11 generally combines CBD resistance with high yields and fine quality, Ruiru 11 sibs present significant variability in terms of resistance to CBD, quality and yields. The varying parentage of Ruiru 11 sibs could be contributing to the observed variation in beverage quality and non-uniform resistance to CBD within the composite cultivar. Besides the genetic differences, the growing environment has a strong effect on yields and quality. The objective of this study was to select for CBD resistance, high cherry yields and good quality within the sibs of Coffea arabica L. composite cultivar, Ruiru 11 by confirming the occurrence of T (Ck-1) gene (for CBD resistance) in Ruiru 11 sibs; evaluating individual Ruiru 11 sibs for high CBD resistance, good bean grades, superior cup quality and high yields; characterizing the genetic diversity of selected Ruiru 11 sibs based on resistance to CBD, cherry yields, raw bean grades, cup quality and biochemical composition; analysing the environmental effect on yields, raw bean quality, cup quality and biochemical composition of Ruiru 11 sibs; determining the relationship between cup quality and biochemical composition of Ruiru 11 sibs and assessing the level of C. canephora genome introgression in Ruiru 11 and its effect on quality and CBD resistance.Microsattelite marker Sat 235 which is reportedly linked to CBD resistance Ck-1 gene from Coffea canephora was used to study the occurrence of the gene in Ruiru 11 sibs and their parental genotypes. The test genotypes were Robusta coffee (C. canephora), non introgressed C. arabica cv. caturra, Ruiru 11 parental genotypes and thirty four (34) Ruiru 11 hybrid sibs. Resistance to CBD was evaluated using hypocotyl inoculation method. Genomic DNA was extracted from lyophilized leaves of the test genotypes following the CTAB method and analysed using Sat 235 microsatellite primer. Results of CBD evaluation were correlated to SSR analysis to determine whether the Ck- 1 gene was co-segregating with resistance. The study observed occurrence of Ck-1 gene in all canephoroid-introgressed resistant genotypes including all the 34 Ruiru 11 sibs. The study also provided further evidence that the fragment amplified by SSR primer Sat 235 is linked to CBD resistance. Field experiments were set up at three locations in Kenya namely Mariene in Meru County, Kisii in Kisii County and Koru in Kericho County. The experiment was laid out in a Randomized Complete Block Design (RCBD) with three replications. Experimental plots consisted of 12 trees each of 34 Ruiru 11 sibs per replication planted at a spacing of 2 m by 1.5 m. Two entries of SL28, one of which was sprayed with fungicides against CBD, were used as checks. Ripe coffee (cherry) was picked during the peak harvesting periods of May to July at Mariene and September to November at Koru and Kisii between 2009 and 2011. The harvested cherries were bulked per replication, weighed and yield data recorded. Cherry processing was conducted following the standard processing procedures outlined in CRF technical circular number 204. Dry coffee beans (parchment) were hulled and graded into different grades based on size, shape and density. Beverage quality was determined by a panel of seven professional xxi coffee tasters following the sensory evaluation procedure Specialty Coffee Association of America (SCAA). For biochemical analyses, caffeine, trigonelline and chlorogenic acids (CGA) were extracted and purified using classical methods and analyzed using High Pressure Liquid Chromatograph (HPLC), while for lipids the material was ground and subjected to Soxhlet extraction using n-hexane. Percentage and count data were arcsine amd log transformed respectiviely before statistical analysis were performed. The data were subjected to Analysis of Variance (ANOVA) using XLSTAT (Version 2012) statistical software at 5% significant level. Assessment of cherry yields demonstrated that there was a greater discrimination between sibs at Koru, followed by Kisii and then Mariene. Combined analysis for all locations showed significant differences between sibs, locations and their interaction. The existence of a high yield variation among Ruiru 11 sibs was an indication of high potential of intra-cultivar selection for yield improvement. The best yielding sibs per location were identified but the ones that consistently recorded high yields were R11- 52, R11-117, R11-131, R11-11, R11-105, R11-142, R11-7, R11-100 and R11-121. Results of the raw coffee quality showed that most of the Ruiru 11 sibs recorded similar or better grades than SL28. The lowest grades were observed at Mariene, while the best grades were observed at Koru. The sibs with the best bean grades were identified as R11- 121, R11-93, R11-142, R11-52 and R11-71. Evaluation of cup quality demonstrated high variation among Ruiru 11 sibs in all the cup quality traits except body. Locational variations were also significant and the sibs were best differentiated in the locations where moderate moisture stress occurred during bean expansion and filling stages. The best sibs per location in terms of cup quality were identified but the ones that consistently recorded high quality were R11-52, R11-117, R11-131, R11-107, R11-121, R11-11, R11- 137 and R11-22. The study further demonstrated the existence of high variation in biochemical composition (CGA, Caffeine, Trigonelline and Lipids) among Ruiru 11 sibs. The growing environment was also found to have an effect on biochemical composition as portrayed by locational variations. Robusta coffee (C. canephora), which is the major source of resistance to CBD in Ruiru 11 has relatively poor beverage quality and therefore its genome introgression is expected to affect beverage quality in Ruiru 11 and related families. Chapter eight of this study attempted to gain insights into C. canephora genome introgression in C. arabica. The plant materials included Robusta coffee (C. canephora), introgressed C. arabica var. Hibrido de Timor (HDT), non introgressed C. arabica var. Caturra, SL28 and K7. These were analysed alongside 34 Ruiru 11 hybrid sibs. Genomic DNA from the test genotypes was amplified with 13 microsatellite primer pairs 12 of which had been pre-selected for introgression studies in Arabica coffee. Any common alleles in Robusta, HDT and Ruiru 11 sibs that were missing in Arabica genotypes were considered as introgressed alleles. Similarly, any alleles that were present in non-introgressed Arabica genotypes but missing in Robusta and HDT but were either absent or present in Ruiru 11 sibs were also considered to result from introgression. The study observed that the level of canephoragenome introgression in Ruiru 11 sibs ranges from 8.7 to 24.14%. However, beverage quality of some introgressed Arabica coffee lines was similar to that of non-introgressed traditional varieties. In conclusion, the study confirmed earlier reports that Ruiru 11 sibs differ in quality aspects, yields and resistance to CBD. Biochemical composition was also found to play a major role in determining the cup quality of coffee. Chemical analysis of green coffe beans can therefore be used as an additional tool for coffee quality evaluation. The study further concluded that there is no relationship between the level of canephoragenome introgression and cup quality of Ruiru 11 sibs. Some Ruiru 11 sibs that combine high yields with good quality were identified including R11-6, R11-11, R11-22, R11-52, R11-100, R11-107, R11-117, R11-121, R11-131, R11-137 and R11-142. Some of these namely R11-11, R11-22, R11-107, and R11-121 had also good resistance to CBD. These sibs are recommended to farmers for adoption and can also be exploited in future breeding programmes for improvement of Ruiru 11 yields, quality and CBD resistance. Key Words: Coffee, Beverage Quality, CBD Resistance, Yields, Introgression, Kenya