Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content.

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers' performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers' effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.

Identification of QTLs Controlling Resistance to Anthracnose Disease in Water Yam (Dioscorea alata).

Anthracnose disease caused by a fungus Colletotrichum gloeosporioides is the primary cause of yield loss in water yam (Dioscorea alata), the widely cultivated species of yam. Resistance to yam anthracnose disease (YAD) is a prime target in breeding initiatives to develop durable-resistant cultivars for sustainable management of the disease in water yam cultivation. This study aimed at tagging quantitative trait loci (QTL) for anthracnose disease resistance in a bi-parental mapping population of D. alata. Parent genotypes and their recombinant progenies were genotyped using the Genotyping by Sequencing (GBS) platform and phenotyped in two crop cycles for two years. A high-density genetic linkage map was built with 3184 polymorphic Single Nucleotide Polymorphism (NSP) markers well distributed across the genome, covering 1460.94 cM total length. On average, 163 SNP markers were mapped per chromosome with 0.58 genetic distances between SNPs. Four QTL regions related to yam anthracnose disease resistance were identified on three chromosomes. The proportion of phenotypic variance explained by these QTLs ranged from 29.54 to 39.40%. The QTL regions identified showed genes that code for known plant defense responses such as GDSL-like Lipase/Acylhydrolase, Protein kinase domain, and F-box protein. The results from the present study provide valuable insight into the genetic architecture of anthracnose resistance in water yam. The candidate markers identified herewith form a relevant resource to apply marker-assisted selection as an alternative to a conventional labor-intensive screening for anthracnose resistance in water yam.

Genetic parameters, prediction, and selection in a white Guinea yam early-generation breeding population using pedigree information.

Better understanding of the genetic control of traits in breeding populations is crucial for the selection of superior varieties and parents. This study aimed to assess genetic parameters and breeding values for six essential traits in a white Guinea yam (Dioscorea rotundata Poir.) breeding population. For this, pedigree-based best linear unbiased prediction (P-BLUP) was used. The results revealed significant nonadditive genetic variances and medium to high (.45-.79) broad-sense heritability estimates for the traits studied. The pattern of associations among the genetic values of the traits suggests that selection based on a multiple-trait selection index has potential for identifying superior breeding lines. Parental breeding values predicted using progeny performance identified 13 clones with high genetic potential for simultaneous improvement of the measured traits in the yam breeding program. Subsets of progeny were identified for intermating or further variety testing based on additive genetic and total genetic values. Selection of the top 5% progenies based on the multi-trait index revealed positive genetic gains for fresh tuber yield (t ha-1), tuber yield (kg plant-1), and average tuber weight (kg). However, genetic gain was negative for tuber dry matter content and Yam mosaic virus resistance in comparison with standard varieties. Our results show the relevance of P-BLUP for the selection of superior parental clones and progenies with higher breeding values for interbreeding and higher genotypic value for variety development in yam.

Marker-assisted selection complements phenotypic screening at seedling stage to identify cassava mosaic disease-resistant genotypes in African cassava populations.

Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The use of genomic-assisted selection at the seedling trial stage would help to reduce the time for release, breeding cost, and resources used, hence increase selection efficiency in cassava breeding programs. Five cassava populations were screened for resistance to CMD during the seedling evaluation trial at 1, 3, and 5 months after planting using a scale of 1-5. The genotypes in the five populations were also screened using six molecular markers linked to the CMD2 gene. The correlation between the phenotypic and marker data was estimated. Based on Cassava Mosaic Disease Severity Score (CMDSS), between 53 and 82% of the progenies were resistant across the populations with an average of 70.5%. About 70% of the progenies were identified to be resistant to the disease across the populations with a range of 62-80% using the marker data. With both marker data and CMDSS combined, 40-60% of the progenies in each population, with an average of 52%, were identified to be resistant to CMD. There was a fairly significant correlation between the marker data and CMDSS in each cassava population with correlation coefficients ranging from 0.2024 to 0.3460 suggesting that novel genes not associated to the markers used might be involved in the resistance to CMD. The resistant genotypes identified in this study with potential for other desirable traits were selected for evaluation at the advanced trial stage thereby shortening the period required for the breeding program.

Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers.

Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = - 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.

Genetic dissection of yield associated traits in a cross between cowpea and yard-long bean (Vigna unguiculata (L.) Walp.) based on DArT markers.

Both cowpea and yard-long bean belong to Vigna unguiculata ssp. unguiculata but have diverged through human induced evolution in sub-Saharan Africa and Asia, respectively. To map the quantitative trait loci (QTLs) for yield associated traits and derive new lines that may combine the attributes of both types, we developed a F2:3 mapping population derived from a cross between cowpea line TVu2185 and yard-long bean line TVu6642. Using DArT markers, a total of 30 QTLs accounting for 1.8-13.0% phenotypic variation was detected for pod and seed traits. Some novel major QTLs for peduncle number per plant (qPeN2.2), pod length (qPoL3), seed breadth (qSB4), length (qSL7.2) and thickness (qST9) identified on chromosomes 2, 3, 4, 7 and 9, respectively, are particularly interesting and need to be validated. Moreover, we confirmed previously reported QTLs for pod length (qPoL8) and 100-seed weight (qSW8) on chromosome 8 and for seed number per pod (qSN9.2) on chromosome 9 suggesting usefulness for marker-assisted-selection purpose. Notably, some QTLs for these traits were clustered especially on chromosomes 5, 7, 8, 9 and 10 indicating the presence of the same QTL or linked loci in these regions. Moreover, the involvement of epistasis was observed for trait expressions, but compared with the main effect QTLs, the phenotypic effects of epistatic-QTLs detected were much less. The present QTL analysis may provide a useful tool for breeders to formulate efficientbreeding strategy for introgression of the desirable alleles for yield related traits in cowpea using molecular markers.

Phenotypic approaches to drought in cassava: review.

Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12-18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.