Genomic and pedigree‐based predictive ability for quality traits in tea (Camellia sinensis (L.) O. Kuntze)

© 2021, The Author(s). Genetic improvement of quality traits in tea (Camellia sinensis (L.) O. Kuntze) through conventional breeding methods has been limited, because tea quality is a difficult and expensive trait to measure. Genomic selection (GS) is suitable for predicting such complex traits, as it uses genome wide markers to estimate the genetic values of individuals. We compared the prediction accuracies of six genomic prediction models including Bayesian ridge regression (BRR), genomic best linear unbiased prediction (GBLUP), BayesA, BayesB, BayesC and reproducing kernel Hilbert spaces models incorporating the pedigree relationship namely; RKHS-pedigree, RKHS-markers and RKHS markers and pedigree (RKHS-MP) to determine the breeding values for 12 tea quality traits. One hundred and three tea genotypes were genotyped using genotyping-by-sequencing and phenotyped using nuclear magnetic resonance spectroscopy in replicated trials. We also compared the effect of trait heritability and training population size on prediction accuracies. The traits with the highest prediction accuracies were; theogallin (0.59), epicatechin gallate (ECG) (0.56) and theobromine (0.61), while the traits with the lowest prediction accuracies were theanine (0.32) and caffeine (0.39). The performance of all the GS models were almost the same, with BRR (0.53), BayesA (0.52), GBLUP (0.50) and RKHS-MP (0.50) performing slightly better than the others. Heritability estimates were moderate to high (0.35–0.92). Prediction accuracies increased with increasing training population size and trait heritability. We conclude that the moderate to high prediction accuracies observed suggests GS is a promising approach in tea improvement and could be implemented in breeding programmes

Genomic selection strategies to increase genetic gain in tea breeding programs

Tea [Camellia sinensis (L.) O. Kuntze] is mainly grown in low‐ to middle‐income countries (LMIC) and is a global commodity. Breeding programs in these countries face the challenge of increasing genetic gain because the accuracy of selecting superior genotypes is low and resources are limited. Phenotypic selection (PS) is traditionally the primary method of developing improved tea varieties and can take over 16 yr. Genomic selection (GS) can be used to improve the efficiency of tea breeding by increasing selection accuracy and shortening the generation interval and breeding cycle. Our main objective was to investigate the potential of implementing GS in tea‐breeding programs to speed up genetic progress despite the low cost of PS in LMIC. We used stochastic simulations to compare three GS‐breeding programs with a Pedigree and PS program. The PS program mimicked a practical commercial tea‐breeding program over a 40‐yr breeding period. All the GS programs achieved at least 1.65 times higher genetic gains than the PS program and 1.4 times compared with Seed‐Ped program. Seed‐GSc was the most cost‐effective strategy of implementing GS in tea‐breeding programs. It introduces GS at the seedlings stage to increase selection accuracy early in the program and reduced the generation interval to 2 yr. The Seed‐Ped program outperformed PS by 1.2 times and could be implemented where it is not possible to use GS. Our results indicate that GS could be used to improve genetic gain per unit time and cost even in cost‐constrained tea‐breeding programs

Root foraging capacity in bambara groundnut (Vigna subterranea (L.) Verdc.) core parental lines depends on the root system architecture during the pre-flowering stage

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Characterizing the morphological variability in root system architecture (RSA) during the sensitive pre-flowering growth stage is important for crop performance. To assess this variation, eight bambara groundnut single genotypes derived from landraces of contrasting geographic origin were selected for root system architecture and rooting distribution studies. Plants were grown in a polyvinyl chloride (PVC) column system under controlled water and nutrient availability in a rainout shelter. Days to 50% plant emergence was characterized during the first two weeks after sowing, while taproot length (TRL), root length (RL), root length density (RLD), branching number (BN), branching density (BD) and intensity (BI), surface area (SA), root volume (RV), root diameter (RDia), root dry weight (RDW), shoot dry weight (SDW), and shoot height (SH) were determined at the end of the experiment, i.e., 35 days after emergence. Genotypes S19-3 and DipC1 sourced from drier regions of sub-Saharan Africa generally had longer taproots and greater root length distribution in deeper (60 to 90 cm) soil depths. In contrast, bambara groundnut genotypes from wetter regions (i.e., Gresik, Lunt, and IITA-686) in Southeast Asia and West Africa exhibited relatively shallow and highly branched root growth closer to the soil surface. Genotypes at the pre-flowering growth stage showed differential root foraging patterns and branching habits with two extremes, i.e., deep-cheap rooting in the genotypes sourced from dry regions and a shallow-costly rooting system in genotypes adapted to higher rainfall areas with shallow soils. We propose specific bambara groundnut genotype as donors in root trait driven breeding programs to improve water capture and use efficiency

Ribosomal DNA variation in landraces of bambara groundnut

The ribosomal DNA (rDNA) is a basic component of all eukaryotic chromosomes which codes for rRNA. The rDNA is made of tandemly repeated units of 18S, 5.8S, 28S, ITS and IGS. The 18S, 5.8S and 28S are coding regions while the ITS and IGS are non coding. The rDNA evolves in a concerted manner such that rDNA units within an individual are almost completely identical making it a useful tool in taxonomic studies. The rDNA marker is used to discriminate between species in the same or different genus. Bambara groundnut is an under-utilized legume that is highly nutritious and adapted to low input farming systems. Despite its potential, Bambara groundnut is still cultivated in the form of landraces, and no true varieties have been developed. Precise estimate of genetic variation and genetic relationship is sine qua non for the development of improved cultivars. About 48 individual seeds (3 each) from seven landraces of Bambara groundnut, 9 wild/cultivated species of other legumes (cowpea, mungbean and groundnut) were used in this study. Analysis of the rDNA gene unit shows genetic variation in the species of the genus Vigna and Arachis. The UPGMA dendrogram constructed separates the plant species in this study into three (3) main clusters. The landraces of Bambara groundnut were placed in two different clusters indicating variation of rDNA gene units between the landraces. The analysis of rDNA gene in this study reveals the presence of genetic variation between the landraces of Bambara groundnut which could be used by scientists and breeders in the production of improved cultivars.Keywords: Ribosomal DNA, Bambara groundnut, ITS, IGS, DNA variationAfrican Journal of Biotechnology Vol. 12(35), pp. 5395-540

A cross-species gene expression marker-based genetic map and QTL analysis in bambara groundnut

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops

Photoperiod control of yield and sink capacity in Bambara groundnut (Vigna subterranea) genotypes

© 2020 The Authors. Food and Energy Security published by John Wiley & Sons Ltd on behalf of Association of Applied Biologists In Bambara groundnut [Vigna subterranea (L) Verdc], long photoperiods can cause a decline in pod and seed number. While negative photoperiod effects on pod yield have been reported, positive effects and the existence of genotypes less sensitive for photoperiod have not been reported. Ten geographically diverse genotypes were evaluated over 3years under short and long photoperiod for yield-related traits (pod number, pod weight, seed number, seed weight, and 100 seed weight), pod growth habit (geocarpic or ageocarpic pods), peduncle elongation and soil penetration, and pod set/abortion. Anatomical sections of gynophores and embryonic pod development of a highly photoperiod sensitive genotype “Ankpa-4” from Nigeria were examined. A strong photoperiodic effect on yield component traits (pod number, pod weight, seed number, seed weight, and 100 seed weight) was observed and with considerable variation between genotypes. Three classes of photoperiod effect on pod yield were identified, (a) qualitative short-day types; (b) quantitative short-day types; and (c) quantitative long-day types. In long photoperiods, above-ground vegetative biomass and the length of lateral branches in some genotypes increased by at least twofold. Morphological and anatomical characterization of gynophores and developing pods of the most sensitive line shows continuous geocarpic growth, but with healthy embryonic pods failing to enlarge after soil penetration. Results from the yield patterns of the three phenotypic classes confirm that pods and seeds are high priority sinks, and long photoperiod alters the balance in assimilate distribution between competing yield forming processes and vegetative sinks. By exploiting the genetic variation characterized here for photoperiod requirement for pod filling, the geographical range of this crop could be extended beyond current growing regions. In the near future, we anticipate that Bambara groundnut will become a significant contributor to global food, nutritional, and environmental security once these photoperiod issues are resolved

Major qtls for trunk height and correlated agronomic traits provide insights into multiple trait integration in oil palm breeding

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Superior oil yield is always the top priority of the oil palm industry. Short trunk height (THT) and compactness traits have become increasingly important to improve harvesting efficiency since the industry started to suffer yield losses due to labor shortages. Breeding populations with low THT and short frond length (FL) are actually available, such as Dumpy AVROS pisifera (DAV) and Gunung Melayu dura (GM). However, multiple trait stacking still remains a challenge for oil palm breeding, which usually requires 12–20 years to complete a breeding cycle. In this study, yield and height increment in the GM × GM (GM-3341) and the GM × DAV (GM-DAV-3461) crossing programs were evaluated and palms with good yield and smaller height increment were identified. In the GM-3341 family, non-linear THT growth between THT_2008 (seven years old) and THT_2014 (13 years old) was revealed by a moderate correlation, suggesting that inter-palm competition becomes increasingly important. In total, 19 quantitative trait loci (QTLs) for THT_2008 (8), oil per palm (O/P) (7) and FL (4) were localized on the GM-3341 linkage map, with an average mapping interval of 2.01 cM. Three major QTLs for THT_2008, O/P and FL are co-located on chromosome 11 and reflect the correlation of THT_2008 with O/P and FL. Multiple trait selection for high O/P and low THT (based on the cumulative effects of positive alleles per trait) identified one palm from 100 palms, but with a large starting population of 1000–1500 seedling per cross, this low frequency could be easily compensated for during breeding selection

Natural Genotypic Variation Underpins Root System Response to Drought Stress in Bambara Groundnut [Vigna subterranea (L.) Verdc.]

Bambara groundnut [Vigna subterranea (L.) Verdc.] is grown in rainfed production systems and suffers from periodic drought stress (DS), leading to yield reductions. Natural genotypic variation for root traits is essential for adaptation to water deficit conditions. However, root traits have not been fully utilised as selection criteria to improve DS in bambara groundnut. The present study explored the natural genotypic variation found in single genotypes of bambara groundnut derived from landraces to identify adaptive differences in tap root length (TRL) and root length density (RLD) in response to DS. A diverse core collection of eight bambara groundnut genotypes from various locations (namely, Gresik, LunT, IITA-686, DodR, S19-3, Tiga nicuru, and Ankpa-4, DipC1), were grown for two seasons (2018 and 2019) in polyvinyl chloride (PVC) columns with well-watered (WW) and 30-day DS treatments. Plant samples were collected at 55 days after emergence (DAE) (30 days of DS) and at 105 DAE (30 days of DS plus 50 days of recovery). Under DS, differential TRL among genotypes at 55 DAE was observed, with DodR recording the longest among genotypes with an increase (1% in 2018) in TRL under DS compared to WW, whereas LunT and IITA-686 showed significant (p < 0.001) decrease in TRL (27 and 25%, respectively, in 2018). Average RLD was observed to have the highest reduction under DS in the 90–110 cm layer (42 and 58%, respectively, in 2018 and 2019). Rainy habitat LunT had limited roots in 2018 and recorded the least (0.06 ± 0.013 cm–3) RLD in 2019. However, dry-habitat DodR showed an increase in the RLD (60–90 cm) under DS compared to WW, while dry-habitat S19-3 densely occupied all depths with RLD of 0.16 ± 0.05 and 0.18 ± 0.01 cm cm–3 in the deepest layer in both seasons, respectively. Reduced RLD under DS showed recovery when the plants were re-watered. These plants were additionally observed to have RLD that surpasses the density in WW at all soil depths at 105 DAE. Also, recovery was shown in Tiga nicuru and DodR (0–30 cm) and IITA-686 (90–110 cm) in 2019. Average RLD under DS treatment was associated with substantial grain yield advantage (R2 = 0.27 and R2 = 0.49, respectively) in 2018 and 2019. An increase in TRL allowed DodR to quickly explore water at a deeper soil depth in response to gradually declining soil water availability. High RLD in genotypes such as DodR, DipC1 and S19-3 also offered adaptive advantage over other genotypes under DS. Variation in intrinsic RLD in deeper soil depths in the studied genotypes determines root foraging capacity when facing DS. This suggests that different agroecological environments to which bambara groundnut is subjected in its natural habitat have promoted a phenotypic differentiation in root systems to adapt to ecotypic conditions, which may help offset the impact of DS. The natural genotypic variation exhibited, especially by DodR, could be exploited to identify potential quantitative trait loci (QTLs) that control deep rooting and root length density

An improved oil palm genome assembly as a valuable resource for crop improvement and comparative genomics in the Arecoideae subfamily

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species—date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)—confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae

Development and interaction between plant architecture and yield-related traits in winged bean (Psophocarpus tetragonolobus (L.) DC.)

Winged bean (P. tetragonolobus (L.) DC.) is a leguminous crop that could contribute towards food security in tropical areas, but whose growth and development is still poorly understood. In order to develop improved individuals for increased green pod and seed productivity, we investigated the factors involved in winged bean plant architecture, development, and their link to a number of yield-related traits. An F2 population was generated from the cross between M3 and FP15 Malaysian accessions and assessed under field conditions in Malaysia. The results showed stem length to be mainly influenced by internode length (rs = .80; p \.01), while multiple genes could be controlling the number of branches, with an average number of branches in the offspring above the highest parent value. The average length of branches appeared to influence the most the finalnumber of pods per plant (rs = .44; p\ .001), while flowering showed potentially transgressive segregation towards earliness, without preventing the potential development of high pod-yielding individuals (rs = - 208; p = .056). Taken together, the results reported here shed light on the interaction between morphological, developmental, and yield-related traits, defining potential targets for developing crop ideotypes to direct breeding programmes for this underutilised crop