Genetic analysis of plant morphology in bambara groundnut (Vigna subterranea (L.) Verdc.)

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an important underutilised legume crop, grown mainly by female subsistence farmers in Africa under traditional low input agricultural systems. Bambara groundnut is known as being of high nutritional value, as an atmospheric nitrogen fixer and to possess high levels of drought, pest and disease tolerance. Bambara groundnut is a predominantly self-pollinated crop and is grown as locally adapted landraces. These are expected to exist as non-identical inbred lines and are generally low yielding. Strategies involving genetic analysis of this species could provide important data for breeding programmes that could enhance food security in Africa. A set of 124 SSR primers designed from different library sources were tested to screen a ‘narrow’ genetic cross (F3) and a ‘wide’ genetic cross (F2) . The former is a cross between domesticated landraces (DipC and Tiga necaru) while the latter is a cross between a domesticated landrace and a wild ancestor (DipC and VSSP11). Residual heterozygosity in the F3 ‘narrow’ cross was confirmed to be around 25% based on 33 polymorphic SSR primers, consistent with an F3 population. A ‘narrow’ cross linkage map was constructed for the first time in bambara groundnut using 269 polymorphic markers (236 DArT and 33 SSR). The map consisted of 238 markers in 21 linkage groups of two or more linked markers, totalling 608.1cM and covering a predicted 54% of the bambara groundnut genome, although the high marker-marker linkage (at 89%) suggests a more comprehensive coverage. QTL analysis was carried out for 73 bulked lines of an F3 population and plants were evaluated for traits in a controlled glasshouse suite and a field trial in Indonesia. Data from single plant analysis of the F2 generation of this cross grown in a controlled environment glasshouse was also used. Most of the QTLs detected were clustered on linkage groups 1, 4 and 12. Major QTLs for internode length and biomass dry weight were detected on LG4 and LG1, respectively, for the FutureCrop glasshouse and field datasets. The highest LOD score of 9.7 was detected for peduncle length and was located within the confidence interval for a QTL for internode length locus. Marker locus bgPabg-596774 was detected to be associated with QTL for six traits; node no./plant, pod no/plant, pod weight, seed no./plant, seed yield and biomass dry weight, on LG1 within one LOD score of confidential interval, potentially suggesting pleiotropic effects of a more limited number (or even one) gene(s). One hundred and fifty-nine additional markers (136 DArT and 23 SSR) were used to improve the existing partial ‘wide’ map (141 AFLP, 1 SSR) constructed in an F2 population of 98 plants. A total of 194 markers were assigned to 20 linkage groups spanning a total of 901 cM. The linkage map derived from the ‘wide’ cross (DipC x VSSP11) had an expected genome coverage of 79.6%. An attempt to combine both maps through 32 common markers allowed a common QTL for days to emergence to be detected in both populations in close association with the common DArT markers 601384 and 601748. The main segregating traits were found to be plant spread, internode length, growth habit, peduncle length, pod weight, seed yield and biomass dry weight. Detecting the same QTL positions for a number of traits, suggested that common underlying genes might be responsible. The QTL-DNA marker associations developed in this study could be used practically for MAS in a future breeding program of this crop

Genetic analysis of plant morphology in bambara groundnut (Vigna subterranea (L.) Verdc.)

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an important underutilised legume crop, grown mainly by female subsistence farmers in Africa under traditional low input agricultural systems. Bambara groundnut is known as being of high nutritional value, as an atmospheric nitrogen fixer and to possess high levels of drought, pest and disease tolerance. Bambara groundnut is a predominantly self-pollinated crop and is grown as locally adapted landraces. These are expected to exist as non-identical inbred lines and are generally low yielding. Strategies involving genetic analysis of this species could provide important data for breeding programmes that could enhance food security in Africa. A set of 124 SSR primers designed from different library sources were tested to screen a ‘narrow’ genetic cross (F3) and a ‘wide’ genetic cross (F2) . The former is a cross between domesticated landraces (DipC and Tiga necaru) while the latter is a cross between a domesticated landrace and a wild ancestor (DipC and VSSP11). Residual heterozygosity in the F3 ‘narrow’ cross was confirmed to be around 25% based on 33 polymorphic SSR primers, consistent with an F3 population. A ‘narrow’ cross linkage map was constructed for the first time in bambara groundnut using 269 polymorphic markers (236 DArT and 33 SSR). The map consisted of 238 markers in 21 linkage groups of two or more linked markers, totalling 608.1cM and covering a predicted 54% of the bambara groundnut genome, although the high marker-marker linkage (at 89%) suggests a more comprehensive coverage. QTL analysis was carried out for 73 bulked lines of an F3 population and plants were evaluated for traits in a controlled glasshouse suite and a field trial in Indonesia. Data from single plant analysis of the F2 generation of this cross grown in a controlled environment glasshouse was also used. Most of the QTLs detected were clustered on linkage groups 1, 4 and 12. Major QTLs for internode length and biomass dry weight were detected on LG4 and LG1, respectively, for the FutureCrop glasshouse and field datasets. The highest LOD score of 9.7 was detected for peduncle length and was located within the confidence interval for a QTL for internode length locus. Marker locus bgPabg-596774 was detected to be associated with QTL for six traits; node no./plant, pod no/plant, pod weight, seed no./plant, seed yield and biomass dry weight, on LG1 within one LOD score of confidential interval, potentially suggesting pleiotropic effects of a more limited number (or even one) gene(s). One hundred and fifty-nine additional markers (136 DArT and 23 SSR) were used to improve the existing partial ‘wide’ map (141 AFLP, 1 SSR) constructed in an F2 population of 98 plants. A total of 194 markers were assigned to 20 linkage groups spanning a total of 901 cM. The linkage map derived from the ‘wide’ cross (DipC x VSSP11) had an expected genome coverage of 79.6%. An attempt to combine both maps through 32 common markers allowed a common QTL for days to emergence to be detected in both populations in close association with the common DArT markers 601384 and 601748. The main segregating traits were found to be plant spread, internode length, growth habit, peduncle length, pod weight, seed yield and biomass dry weight. Detecting the same QTL positions for a number of traits, suggested that common underlying genes might be responsible. The QTL-DNA marker associations developed in this study could be used practically for MAS in a future breeding program of this crop

Integrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] and their syntenic relationships among closely related legumes

Background Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata). From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. Results Two individual intraspecific linkage maps consisting of DArTseq markers were constructed in two bambara groundnut (2n = 2x = 22) segregating populations: 1) The genetic map of Population IA was derived from F2 lines (n = 263; IITA686 x Ankpa4) and covered 1,395.2 cM across 11 linkage groups; 2) The genetic map of Population TD was derived from F3 lines (n = 71; Tiga Nicuru x DipC) and covered 1,376.7 cM across 11 linkage groups. A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial ‘pseudo’ physical map for bambara groundnut. A good correspondence was observed at the macro synteny level, particularly to the common bean genome. A test using the QTL location of an agronomic trait in one of the bambara groundnut maps allowed the corresponding flanking positions to be identified in common bean, mung bean and adzuki bean, demonstrating the possibility of identifying potential candidate genes underlying traits of interest through the conserved syntenic physical location of QTL in the well annotated genomes of closely related species. Conclusions The approach of adding pre-selected common markers in both populations before genetic map construction has provided a translational framework for potential identification of candidate genes underlying a QTL of trait of interest in bambara groundnut by linking the positions of known genetic effects within the underutilised species to the physical maps of other well-annotated legume species, without the need for an existing whole genome sequence of the study species. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the minor crop species. Such minor crops will be required to play an important role in future agriculture under the effects of climate change

Genetic analysis of plant morphology in bambara groundnut (Vigna subterranea (L.) Verdc.)

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an important underutilised legume crop, grown mainly by female subsistence farmers in Africa under traditional low input agricultural systems. Bambara groundnut is known as being of high nutritional value, as an atmospheric nitrogen fixer and to possess high levels of drought, pest and disease tolerance. Bambara groundnut is a predominantly self-pollinated crop and is grown as locally adapted landraces. These are expected to exist as non-identical inbred lines and are generally low yielding. Strategies involving genetic analysis of this species could provide important data for breeding programmes that could enhance food security in Africa. A set of 124 SSR primers designed from different library sources were tested to screen a ‘narrow’ genetic cross (F3) and a ‘wide’ genetic cross (F2) . The former is a cross between domesticated landraces (DipC and Tiga necaru) while the latter is a cross between a domesticated landrace and a wild ancestor (DipC and VSSP11). Residual heterozygosity in the F3 ‘narrow’ cross was confirmed to be around 25% based on 33 polymorphic SSR primers, consistent with an F3 population. A ‘narrow’ cross linkage map was constructed for the first time in bambara groundnut using 269 polymorphic markers (236 DArT and 33 SSR). The map consisted of 238 markers in 21 linkage groups of two or more linked markers, totalling 608.1cM and covering a predicted 54% of the bambara groundnut genome, although the high marker-marker linkage (at 89%) suggests a more comprehensive coverage. QTL analysis was carried out for 73 bulked lines of an F3 population and plants were evaluated for traits in a controlled glasshouse suite and a field trial in Indonesia. Data from single plant analysis of the F2 generation of this cross grown in a controlled environment glasshouse was also used. Most of the QTLs detected were clustered on linkage groups 1, 4 and 12. Major QTLs for internode length and biomass dry weight were detected on LG4 and LG1, respectively, for the FutureCrop glasshouse and field datasets. The highest LOD score of 9.7 was detected for peduncle length and was located within the confidence interval for a QTL for internode length locus. Marker locus bgPabg-596774 was detected to be associated with QTL for six traits; node no./plant, pod no/plant, pod weight, seed no./plant, seed yield and biomass dry weight, on LG1 within one LOD score of confidential interval, potentially suggesting pleiotropic effects of a more limited number (or even one) gene(s). One hundred and fifty-nine additional markers (136 DArT and 23 SSR) were used to improve the existing partial ‘wide’ map (141 AFLP, 1 SSR) constructed in an F2 population of 98 plants. A total of 194 markers were assigned to 20 linkage groups spanning a total of 901 cM. The linkage map derived from the ‘wide’ cross (DipC x VSSP11) had an expected genome coverage of 79.6%. An attempt to combine both maps through 32 common markers allowed a common QTL for days to emergence to be detected in both populations in close association with the common DArT markers 601384 and 601748. The main segregating traits were found to be plant spread, internode length, growth habit, peduncle length, pod weight, seed yield and biomass dry weight. Detecting the same QTL positions for a number of traits, suggested that common underlying genes might be responsible. The QTL-DNA marker associations developed in this study could be used practically for MAS in a future breeding program of this crop.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Construction of a genetic linkage map and QTL analysis in bambara groundnut (Vigna subterranea (L) Verdc.)

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilised legume which has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could be used for variety development and genetic studies. We reported here the construction of the first genetic linkage map of bambara groundnut using a F3 population derived from a ‘narrow’ cross between two domesticated landraces (Tiga Nicaru and DipC) with marked divergence in phenotypic traits. The map consists of 238 DArT array and SSR based markers in 21 Linkage Groups (LGs) with a total genetic distance of 608.3 cM. In addition, phenotypic traits were evaluated for a Quantitative Trait Loci (QTL) analysis over two generations. A total of 36 significant QTLs were detected for 19 traits. The phenotypic effect explained by a single QTL ranged from 11.6% to 49.9%. Two stable QTLs were mapped for internode length and growth habit. The identified QTLs could be significant for marker-assisted selection (MAS) in bambara groundnut breeding programmes.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author