Field evaluation of the impact of cocoa swollen shoot virus disease infection on yield traits of different cocoa (Theobroma cacao L.) clones in Ghana.

Cocoa swollen shoot virus disease (CSSVD) is a major disease of cacao (Theobroma cacao L.) in Ghana and other West African countries that grow the crop. Attempts to develop resistant varieties since the discovery of the disease in 1936 have yielded little success. Recently, planting materials that are tolerant to the disease have been recommended for planting in areas with high CSSVD prevalence. However, the effect of CSSVD on yield component traits of most cacao clones including the tolerant varieties has not been well studied. To investigate the impact of CSSVD on these traits, reduction in bean weight (BW), number of beans per pod (NoBP) and dry bean yield (DBY) between symptomless and symptomatic trees, and disease incidence (DI) among 210 different cacao clones were evaluated. The clones were transplanted in June 2010 following a randomised complete block design with four replications consisting of three trees per clone per block. Response of the clones to CSSVD incidence had 180 of the genotypes having < 50% symptoms. Clones of Contanama, Iquitos, Marañon, Nanay and unknown derived from Upper Amazon parentage had less DI at the end of the study. The CSSVD effect (symptomless vs. symptomatic) was significant (p < 0.05) for DBY and NoBP, and the symptomless trees surpassed on average their symptomatic trees by 21.17% for DBY. Some of the best-performing clones identified under natural CSSVD infection were; COCA 3348/52 and GU 219/V among the underrepresented clones, B 36, ICS 40, NA 33 x IMC 67, T30/628, T60/887, T63/971, T 81/1879 and T 82/503 among those that combine high DBY with low yield reduction, and NA 124, T17/358, T35/78, T57/305, T63/971 x SCA 6, T65/239, T76/1835 and T82/2294 among those that combine high DBY with no disease incidence. Their inclusion in breeding programs that seek to develop resistant CSSVD varieties or deployment as planting materials in endemic areas to improve yield production in Ghana is recommended on the basis of the present observations.

Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay.

Accurate genotype identification is imperative for effective use of Coffea canephora L. germplasm to breed new varieties with tolerance or resistance to biotic and abiotic stresses (including moisture stress and pest and disease stresses such as coffee berry borer and rust) and for high yield and improved cup quality. The present study validated 192 published single nucleotide polymorphism (SNP) markers and selected a panel of 120 loci to examine parentage and labeling errors, genetic diversity, and population structure in 400 C. canephora accessions assembled from different coffee-producing countries and planted in a field gene bank in Ghana. Of the 400 genotypes analyzed, both synonymous (trees with same SNP profiles but different names, 12.8%) and homonymous (trees with same name but different SNP profiles, 5.8%) mislabeling were identified. Parentage analysis showed that 33.3% of the progenies derived from controlled crossing and 0% of the progenies derived from an open pollinated biclonal seed garden had parentage (both parents) corresponding to breeder records. The results suggest mislabeling of the mother trees used in seed gardens and pollen contamination from unwanted paternal parents. After removing the duplicated accessions, Bayesian clustering analysis partitioned the 270 unique genotypes into two main populations. Analysis of molecular variance (AMOVA) showed that the between-population variation accounts for 41% of the total molecular variation and the genetic divergence was highly significant (Fst = 0.256; P < 0.001). Taken together, our results demonstrate the effectiveness of using the selected SNP panel in gene bank management, varietal identification, seed garden management, nursery verification, and coffee bean authentication for C. canephora breeding programs.

Fine-mapping and identification of a candidate gene underlying the d2 dwarfing phenotype in pearl millet, Cenchrus americanus (L.) Morrone.

Pearl millet is one of the most important subsistence crops grown in India and sub-Saharan Africa. In many cereal crops, reduced height is a key trait for enhancing yield, and dwarf mutants have been extensively used in breeding to reduce yield loss due to lodging under intense management. In pearl millet, the recessive d2 dwarfing gene has been deployed widely in commercial germplasm grown in India, the United States, and Australia. Despite its importance, very little research has gone into determining the identity of the d2 gene. We used comparative information, genetic mapping in two F2 populations representing a total of some 1500 progeny, and haplotype analysis of three tall and three dwarf inbred lines to delineate the d2 region by two genetic markers that, in sorghum, define a region of 410 kb with 40 annotated genes. One of the sorghum genes annotated within this region is ABCB1, which encodes a P-glycoprotein involved in auxin transport. This gene had previously been shown to underlie the economically important dw3 dwarf mutation in sorghum. The cosegregation of ABCB1 with the d2 phenotype, its differential expression in the tall inbred ICMP 451 and the dwarf inbred Tift 23DB, and the similar phenotype of stacked lower internodes in the sorghum dw3 and pearl millet d2 mutants suggest that ABCB1 is a likely candidate for d2.