Development of expressed sequence tags-simple sequence repeats (EST-SSRs) for Musa and their applicability in authentication of a Musa breeding population

Maintaining identity of clones is essential in breeding programs. New EST-SSR markers have been developed for banana and used to screen a diploid population for clonal identity. A total of 410 primer pairs were designed from an EST database, validated using polyacrylamide gel electrophoresis (PAGE) and a subset was optimized for accurate genotyping on a capillary genetic analyzer. Combining PAGE and capillary electrophoresis, about 44% of the designed primers were informative in the diploid population. The majority of markers produced two alleles as expected in a diploid population. However, some showed three to four alleles, possibly indicating closely-related members of gene families. Screening of field samples using SSR markers revealed genotype identity issues in the target population. The present study demonstrates the applicability of SSRs in the  establishment of parentage and relatedness between accessions. The newly-developed SSRs will be valuable tools in the understanding of Musa genetics, in marker-trait associations, thereby enhancing the effectiveness of breeding programs.Key words: EST, SSRs, markers, Musa, breeding

Construction of a DArT-seq marker–based genetic linkage map and identification of QTLs for yield in tea (Camellia sinensis (L.) O. Kuntze)

As the second most consumed non-alcoholic beverage, the tea plant (Camellia sinensis) has high economic value. Tea improvement efforts that largely target economic traits such as yield have traditionally relied on conventional breeding approaches. The tea plant’s perennial nature and its long generation time make conventional approaches time-consuming and labour-intensive. Biotechnology provides a complementary tool for accelerating tea improvement programmes through marker-assisted selection (MAS). Quantitative trait loci (QTLs) identified on linkage maps are an essential prerequisite to the implementation of MAS. QTL analysis was performed on yield data over 3 years (2010–2012) across two sites (Timbilil and Kangaita, in Kenya), based on two parental framework linkage maps arising from a population of 261 F1 progeny, derived from a reciprocal cross between GW Ejulu and TRFK 303/577. The maps contain 15 linkage groups each, this corresponds to the haploid chromosome number of tea (2n=2x=30). The total length of the parental maps was 1028.1 cM for GW Ejulu and 1026.6 cM for TRFK 303/577 with an average locus spacing of 5.5 cM and 5.4 cM, respectively. A total of 13 QTLs were identified over the three measurement years. The 13 QTLs had LOD values ranging from 1.98 to 7.24 and explained 3.4% to 12% of the phenotypic variation. The two sites had seven mutually detected QTLs.http://link.springer.com/journal/11295hj2022BiochemistryGeneticsMicrobiology and Plant Patholog

The genetic basis and nutritional benefits of pigmented rice grain

Open Access Journal; Published online: 13 Mar 2020Improving the nutritional quality of rice grains through modulation of bioactive compounds and micronutrients represents an efficient means of addressing nutritional security in societies which depend heavily on rice as a staple food. White rice makes a major contribution to the calorific intake of Asian and African populations, but its nutritional quality is poor compared to that of pigmented (black, purple, red orange, or brown) variants. The compounds responsible for these color variations are the flavonoids anthocyanin and proanthocyanidin, which are known to have nutritional value. The rapid progress made in the technologies underlying genome sequencing, the analysis of gene expression and the acquisition of global ‘omics data, genetics of grain pigmentation has created novel opportunities for applying molecular breeding to improve the nutritional value and productivity of pigmented rice. This review provides an update on the nutritional value and health benefits of pigmented rice grain, taking advantage of both indigenous and modern knowledge, while also describing the current approaches taken to deciphering the genetic basis of pigmentation

Technological innovations for improving cassava production in sub-Saharan Africa

Open Access Journal; Published online: 21 Jan 2021Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production

Low-cost, handheld near-infrared spectroscopy for root dry matter content prediction in cassava

Open Access Journal; Published online: 31 Mar 2022Over 800 million people across the tropics rely on cassava (Manihot esculenta Crantz) as a major source of calories. While the root dry matter content (RDMC) of this starchy root crop is important for both producers and consumers, characterization of RDMC by traditional methods is time-consuming and laborious for breeding programs. Alternate phenotyping methods have been proposed but lack the accuracy, cost, or speed ultimately needed for cassava breeding programs. For this reason, we investigated the use of a low-cost, handheld near-infrared spectrometer (740–1070 nm) for field-based RDMC prediction in cassava. Oven-dried measurements of RDMC were paired with 21,044 scans of roots of 376 diverse genotypes from 10 field trials in Nigeria and grouped into training and test sets based on cross-validation schemes relevant to plant breeding programs. Mean partial least squares regression model performance ranged from R2P = 0.62–0.89 for within-trial predictions, which is within the range achieved with laboratory-grade spectrometers in previous studies. Relative to other factors, model performance was highly affected by the inclusion of samples from the same environment in both the training and test sets. With appropriate model calibration, the tested spectrometer will allow for field-based collection of spectral data with a smartphone for accurate RDMC prediction and potentially other quality traits, a step that could be easily integrated into existing harvesting workflows of cassava breeding programs

Unravelling marker trait associations linking nutritional value with pigmentation in rice seed

Open Access JournalWhile considerable breeding effort has focused on increasing the yields of staple crops such as rice and the levels of micronutrients such as iron and zinc, breeding to address the problems of the double-burden of malnutrition has received less attention. Pigmented rice has higher nutritional value and greater health benefits compared to white rice. However, the genetic associations underlying pericarp coloration and accumulation of nutritionally valuable compounds is still poorly understood. Here we report the targeted genetic analysis of 364 rice accessions, assessing the genetic relationship between pericarp coloration (measured using multi-spectral imaging) and a range of phenolic compounds with potential nutritional and health-promoting characteristics. A genome-wide association study resulted in the identification of over 280 single nucleotide polymorphisms (SNPs) associated with the traits of interest. Many of the SNPs were associated with more than one trait, colocalization occurring between nutritional traits, and nutritional and color-related traits. Targeted association analysis identified 67 SNPs, located within 52 candidate genes and associated with 24 traits. Six haplotypes identified within the genes Rc/bHLH17 and OsIPT5 indicated that these genes have an important role in the regulation of a wide range of phenolic compounds, and not only those directly conferring pericarp color. These identified genetic linkages between nutritionally valuable phenolic compounds and pericarp color present not only a valuable resource for the enhancement of the nutritional value of rice but an easy method of selection of suitable genotypes

Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm

Genome-wide association analysis of bacterial blight resistance to nine Xoo strains in 198 indica genotypes based on Efficient Mixed-Model Association eXpedited Model (EMMAX). Manhattan plots for nine Xoo strains (a) PXO61, (b) PXO86, (c) PXO79, (d) PXO71, (e) PXO112, (f) PXO99, (g) PXO339, (h) PXO349, and (i) PXO341. X-axis shows the SNPs along each chromosome; y axis is the − log10 (P-value) for the association. Significant SNPs are those beyond the red line having P-value < 1 × 10 −5. Quantile-quantile plots for nine Xoo strains (j) PXO61, (k) PXO86, (l) PXO79, (m) PXO71, (n) PXO112, (o) PXO99, (p) PXO339, (q) PXO349, and (r) PXO341. (PPTX 521 kb

Conversion and validation of uniplex SNP markers for selection of resistance to Cassava Mosaic Disease in Cassava breeding programs

Open Access journal; Published online: 25 Feb 2021Cassava mosaic disease (CMD) is a major viral disease adversely affecting cassava production in Africa and Asia. Genomic regions conferring resistance to the disease have been mapped in African cassava germplasm through biparental quantitative trait loci (QTL) mapping and genome-wide association studies. To facilitate the utilization of these markers in breeding pipelines to support selections, proof-of-concept technical and biological validation research was carried out using independent pre-breeding and breeding populations. Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) assays were designed from three single nucleotide polymorphism (SNP) markers linked to a major resistance locus on chromosome 12 (S12_7926132, S12_7926163) and a minor locus on chromosome 14 (S14_4626854). The designed assays were robust and easy to score with >99% genotype call rate. The overall predictive accuracy (proportion of true positives and true negatives) of the markers (S12_7926132 and S14_4626854) was 0.80 and 0.78 in the pre-breeding and breeding population, respectively. On average, genotypes that carried at least one copy of the resistant allele at the major CMD2 locus had a significantly higher yield advantage. Nevertheless, variation was observed in prediction accuracies for the major locus (S12_7926132) among sub-families from the two populations, suggesting the need for context-specific utilization, for example, by screening for co-segregation of favorable SNP alleles with resistance in the parents being used for crosses. Availability of these validated SNP markers on the uniplex KASP genotyping platform represents an important step in translational genetics toward marker-assisted selection to accelerate introgression of favorable resistant alleles in breeding populations

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

Open Access Journal; Published online: 12 Oct 2022Provitamin 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

Breeding schemes: what are they, how to formalize them, and how to improve them?

Open Access Journal; Published online: 21 Jan 2022Formalized breeding schemes are a key component of breeding program design and a gateway to conducting plant breeding as a quantitative process. Unfortunately, breeding schemes are rarely defined, expressed in a quantifiable format, or stored in a database. Furthermore, the continuous review and improvement of breeding schemes is not routinely conducted in many breeding programs. Given the rapid development of novel breeding methodologies, it is important to adopt a philosophy of continuous improvement regarding breeding scheme design. Here, we discuss terms and definitions that are relevant to formalizing breeding pipelines, market segments and breeding schemes, and we present a software tool, Breeding Pipeline Manager, that can be used to formalize and continuously improve breeding schemes. In addition, we detail the use of continuous improvement methods and tools such as genetic simulation through a case study in the International Institute of Tropical Agriculture (IITA) Cassava east-Africa pipeline. We successfully deploy these tools and methods to optimize the program size as well as allocation of resources to the number of parents used, number of crosses made, and number of progeny produced. We propose a structured approach to improve breeding schemes which will help to sustain the rates of response to selection and help to deliver better products to farmers and consumers