Hussein Shimelis

Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)

Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeonpea breeding.

Breeding wheat for drought tolerance: Progress and technologies

Abstract Recurrent drought associated with climate change is among the principal constraints to global productivity of wheat ( Triticum aestivum (L.) and T. turgidum (L.)). Numerous efforts to mitigate drought through breeding resilient varieties are underway across the world. Progress is, however, hampered because drought tolerance is a complex trait that is controlled by many genes and its full expression is affected by the environment. Furthermore, wheat has a structurally intricate and large genome. Consequently, breeding for drought tolerance requires the integration of various knowledge systems and methodologies from multiple disciplines in plant sciences. This review summarizes the progress made in dry land wheat improvement, advances in knowledge, complementary methodologies, and perspectives towards breeding for drought tolerance in the crop to create a coherent overview. Phenotypic, biochemical and genomics-assisted selection methodologies are discussed as leading research components used to exploit genetic variation. Advances in phenomic and genomic technologies are highlighted as options to circumvent existing bottlenecks in phenotypic and genomic selection, and gene transfer. The prospects of further integration of these technologies with other omics technologies are also provided.

Screening of Bread Wheat Genotypes for Drought Tolerance Using Phenotypic and Proline Analyses

Drought stress is one of the leading constraints to wheat (Triticum aestivum L.) production globally. Breeding for drought tolerance using novel genetic resources is an important mitigation strategy. This study aimed to determine the level of drought tolerance among diverse bread wheat genotypes using agronomic traits and proline analyses and to establish correlation of proline content and agronomic traits under drought-stress conditions in order to select promising wheat lines for breeding. Ninety-six diverse genotypes including 88 lines from the International Maize and Wheat Improvement Center (CIMMYT)s heat and drought nurseries, and eight local checks were evaluated under greenhouse and field conditions during 2014/15 and 2015/16 making four testing environments. The following phenotypic traits were collected after stress imposed during the heading to anthesis period: the number of days to heading (DTH), days to maturity (DTM), productive tiller number (TN), plant height (PH), spike length (SL), spikelet per spike (SPS), kernels per spike (KPS), thousand kernel weight (TKW) and grain yield (GY) and proline content (PC). Analysis of variance, Pearsons correlation coefficient, principal component and stress tolerance index were calculated. Genotypes with high yield performance under stressed and optimum conditions maintained high values for yield components. Proline content significantly increased under stress, but weakly correlated with agronomic traits under both optimal and water limited conditions. The positive correlation observed between grain yield and proline content under-drought stress conditions provides evidence that proline accumulation might ultimately be considered as a tool for effective selection of drought tolerant genotypes. The study selected 12 genotypes with high grain yields under drought stressed conditions and favorable adaptive traits useful for breeding.

Genome-wide association analysis of agronomic traits in wheat under drought-stressed and non-stressed conditions

This study determined the population structure and genome-wide marker-trait association of agronomic traits of wheat for drought-tolerance breeding. Ninety-three diverse bread wheat genotypes were genotyped using the Diversity Arrays Technology sequencing (DArTseq) protocol. The number of days-to-heading (DTH), number of days-to-maturity (DTM), plant height (PHT), spike length (SPL), number of kernels per spike (KPS), thousand kernel weight (TKW) and grain yield (GYLD), assessed under drought-stressed and non-stressed conditions, were considered for the study. Population structure analysis and genome-wide association mapping were undertaken based on 16,383 silico DArTs loci with < 10% missing data. The population evaluated was grouped into nine distinct genetic structures. Inter-chromosomal linkage disequilibrium showed the existence of linkage decay as physical distance increased. A total of 62 significant (P < 0.001) marker-trait associations (MTAs) were detected explaining more than 20% of the phenotypic variation observed under both drought-stressed and non-stressed conditions. Significant (P < 0.001) MTA event(s) were observed for DTH, PHT, SPL, SPS, and KPS; under both stressed and non-stressed conditions, while additional significant (P < 0.05) associations were observed for TKW, DTM and GYLD under non-stressed condition. The MTAs reported in this population could be useful to initiate marker-assisted selection (MAS) and targeted trait introgression of wheat under drought-stressed and non-stressed conditions, and for fine mapping and cloning of the underlying genes and QTL.

Response of Potato Genotypes to Bacterial Wilt Caused by Ralstonia Solanacearum (Smith)(Yabuuchi et al.) In the Tropical Highlands

Potato varietal resistance to bacterial wilt disease caused by Ralstonia solanacearum Yabuuchi et al., (Microbiology and Immunology 39:897–904, 1995) is the best management of the disease. Because the causal pathogen exhibits strong host-pathogen-environment interaction, screening the potential parents for resistance under the target growing environmental conditions is the first important step for effective resistance breeding. The objective of this study was to determine the response to bacterial wilt of selected potato genotypes currently grown by farmers in Kenya and candidate clones from the International Potato Center to identify parents that can be used in the local breeding program to develop resistant cultivars. A study was carried out at Kabete, Kenya for three consecutive seasons between November 2011 and February 2013. Thirty six potato genotypes were planted on an inoculated field at the Kenya Agricultural Research Institute (KARI), Kabete using alpha lattice experimental design with three replications. Data collected were days from planting to onset of wilting (DTOW), bacterial wilt incidence (BWI), total tuber weight (ton ha−1) (TTW), total tuber numbers/hectare (TTN), proportion of ware sized tubers (PWTTW), proportion of symptomatic tubers based on weight (PSTTW), proportion of symptomatic tubers based on tuber numbers (PSTTN) and latent infection (LI) of the tubers. Almost, all the potato genotypes evaluated in this study were susceptible to bacerial wilt. Ranking of genotypes based on resistance differed among the three seasons. On average, the three most resistant genotypes were Kenya Karibu, Kenya Sifa and Ingabire. The study identified eight potato genotypes (Meru, Ingabire, Kenya Karibu, Sherekea, Kihoro, Tigoni, Bishop Gitonga and Cangi) to be used as promising parents for subsequent crosses. The chosen genotypes are prolific in pollen production and popularly grown by Kenyan farmers.ResumenLa Resistencia varietal de la papa a la enfermedad de la marchitez bacteriana, causada por Ralstonia solanacearum Yabuuchi et al., (Microbiology and Immunology 39:897–904, 1995), es el mejor manejo de la enfermedad. Considerando que el agente patógeno causal presenta una interacción fuerte hospedante-patógeno-ambiente, las pruebas de padres potenciales para resistencia bajo condiciones ambientales de crecimiento enfocadas, es el primer paso importante para el mejoramiento efectivo para la resistencia. El objetivo de este estudio fue determinar la respuesta a la marchitez bacteriana de genotipos de papa selectos que actualmente se cultivan por productores en Kenia y clones candidatos del Centro Internacional de la Papa, para identificar padres que pudieran usarse en el programa local de mejoramiento para desarrollar variedades resistentes. Un estudio se efectuó en Kabete, Kenia, durante tres ciclos consecutivos entre noviembre de 2011 y febrero de 2013. Se plantaron 36 genotipos de papa en un campo inoculado en el Instituto de Investigaciones Agrícolas de Kenia (KARI). En Kabete se usó un diseño de látice alfa con tres repeticiones. Los datos tomados fueron los días desde la siembra hasta el establecimiento del marchitamiento (DTOW), incidencia de la marchitez bacteriana (BWI), peso total de tubérculo (ton ha-1) (TTW), número total de tubérculos/ha (TTN), proporción de tubérculos de tamaño comercial (PWTTW), proporción de tubérculos sintomáticos con base en el peso (PSTTW), proporción de tubérculos sintomáticos con base en el número de tubérculos (PSTTN) e infección latente (LI) de los tubérculos. Casi todos los genotipos de papa evaluados en este estudio fueron susceptibles al marchitamiento bacteriano. La clasificación de los genotipos con base en la resistencia varió entre los tres ciclos de cultivo. En promedio, Los tres genotipos más resistentes fueron Kenya Karibu, Kenya Sifa, e Ingabire. El estudio identificó ocho genotipos de papa ((Meru, Ingabire, Kenya Karibu, Sherekea, Kihoro, Tigoni, Bishop Gitonga y Cangi) para usarse como progenitores prometedores para cruzas subsecuentes. Los genotipos seleccionados son prolíficos en producción de polen y se cultivan popularmente por los productores kenianos.

Genetic interrelationships among medium to late maturing tropical maize inbred lines using selected SSR markers

Understanding the genetic relationships among breeding lines is fundamental in crop improvement programs. The objectives of this study were to apply selected polymorphic single sequence repeat (SSR) DNA markers and cluster medium to late maturing tropical elite maize inbred lines for effective hybrid breeding. Twenty elite inbred lines were genotyped with 20 SSR markers. The analysis detected a total of 108 alleles. The unweighted pair group method with arithmetic mean allocated the inbred lines into five clusters consistent with the known pedigrees. The tested inbred lines that were adapted to mid-altitude, sub-humid agro-ecologies were classified in different clusters, except for a few discrepancies. The greatest genetic distance was identified between the clusters of lines CML-202 and Gibe-1-91-1-1-1-1. The analysis determined the genetic grouping present in the source population, which will assist in effective utilization of the lines in tropical hybrid maize breeding programs to exploit heterosis.

Genetic diversity of bottle gourd (Lagenaria siceraria (Molina) Standl.) landraces of South Africa assessed by morphological traits and simple sequence repeat markers

Bottle gourd (Lagenaria siceraria (Molina) Standl.) is an important crop in rural communities in South Africa but it remains under-researched. The objective of this study was to assess the genetic diversity present amongst bottle gourd landraces grown by smallholder farmers in South Africa using morphological traits and 11 selected polymorphic simple sequence repeat (SSR) markers. Marked phenotypic differences were observed amongst bottle gourd landraces. Principal component analysis on quantitative traits identified seven principal components, which accounted for 87% of the total variation. Number of alleles varied from 3 to 9 with a mean of 6 per SSR locus. Number of effective alleles ranged from 1.99 to 6.72 with a mean of 3.75. Shannons information index varied from 0.95 to 2.01 with a mean of 1.41. Expected heterozygosity values ranged from 0.5 to 0.87 with a mean of 0.71 with polymorphic information content values of 0.5 to 0.85 and a mean of 0.7. Morphological traits and SSR marker analyses showed a significant correlation in clustering the landraces. The present study demonstrated the presence of genetic diversity amongst bottle gourd landrace collections from South Africa useful for strategic improvement, direct production or conservation.

Principal agronomic and seed oil traits in the industrial oil crop vernonia (Centrapalus pauciflorus var. ethiopica)

Vernonia (Centrapalus pauciflorus) is potentially a new crop that could offer naturally epoxidised industrial oil. The objective of this study was to apply principal component analyses on agronomic traits, seed oil and fatty acid compositions in vernonia to identify the most influential and representative characters for effective breeding. Field evaluations, and oil and fatty acid analyses were conducted using 36 diverse accessions of C. pauciflorus var. ethiopica. Two principal components (PC) were determined contributing 79.26% of the variation among the agronomic traits. PC1 explained 59.71% of the variation represented by the numbers of productive primary seed heads and seed yield. PC2 contributed at 19.55% highly correlated with the number of productive secondary heads. The principal component analysis on seed oil and fatty acid compositions allocated three components explaining 75% of the variation. PC1, PC2 and PC3 contributed 41%, 19% and 15%, respectively, to the total variance. The principal traits were seed oil content, palmitic acid and stearic acid in PC1, oleic acid in PC2 and arachidic acid in PC3. The selected traits may help in developing appropriate and effective breeding strategies for the improvement, large-scale production and germplasm conservation of vernonia.

Phenotypic characterisation of sweetpotato genotypes grown in East and Central Africa

Identification of genetic variability and interrelationships among germplasm collections is fundamental to select parents with complementary traits for plant breeding programmes. The aim of this study was to characterise and identify breeding parents among 54 sweetpotato genotypes grown in Rwanda, East and Central Africa. Genotypes were field-evaluated using 26 phenotypic traits under a 9 × 6 unbalanced alpha lattice experimental design with three replications at Karama and Rubona stations in Rwanda. There were significant (P < 0.01) genotype by site interaction and genotype and site effects on flowering rate, yields of storage roots and vines, harvest index, weight of the largest root per plant and dry matter content. Genotypes K513261, Kwezikumwe, 8-1038 and 2005-110 showed the highest flowering rates of 44.97%, 20.63%, 19.05% and 14.82%, respectively. Suitable genotypes such as K513261, Purple 297, Kwezikumwe and New Kawogo were identified with high storage root yields at 31.90, 28.60, 28.16 and 27.11 t ha−1, respectively. Genotypes Ukerewe, 2005-103, Meresiyana and Mvugamo showed the highest mean dry matter content at 36.52%, 35.53%, 35.31% and 34.04%, respectively. Overall, genotypes K513261, Kwezikumwe, 2005-020, OTADA 24, SPK004, Ukerewe, 2005-110 and 2005-034 were identified as potential breeding parents with superior storage root yield and dry matter content.

Host-status and host-sensitivity of wild Cucumis species to Meloidogyne incognita race 4

Abstract Wild watermelon (Cucumis africanus) and wild cucumber (Cucumis myriocarpus), which are highly resistant to the southern root-knot nematode (Meloidogyne incognita) race 2, have the potential for serving as seedling rootstocks for the highly nematode-susceptible watermelon (Citrullus lanatus) cultivars. In South Africa, due to high labour costs, most cotton farmers are turning to watermelon production. In these regions, there is high incidence of M. incognita race 4. A pot experiment in the greenhouse was, therefore, initiated to investigate the host-status and host-sensitivity of Cucumis africanus and Cucumis myriocarpus to M. incognita race 4, when inoculated with 0, 200, 600, 100, 1400, 1800 and 2200 eggs and second-stage juveniles (J2s). At harvest, 56 days after inoculation, the reproductive factor values at all levels of inoculation were less than one. Penetration indices on both plant species were greater than one, suggesting that the resistance was post-infectional and therefore, introgressible. Sex (male: female) ratios of M. incognita race 4 on the two Cucumis species were greater than one, suggesting that more J2s were converted into males. Infection of Cucumis species by the test nematode had no effect on yield components of the two plant species due to poor feeding sites. The two Cucumis species were, therefore, resistant to M. incognita race 4, with post-infectional resistance, where the sex ratio was skewed towards maleness. Thus, the two Cucumis species have the potential to be used as nematode-resistant rootstocks in watermelon production.