An integrated molecular and conventional breeding scheme for enhancing genetic gain in maize in Africa

Open Access Journal; Published online: 06 Nov 2019Maize production in West and Central Africa (WCA) is constrained by a wide range of interacting stresses that keep productivity below potential yields. Among the many problems afflicting maize production in WCA, drought, foliar diseases, and parasitic weeds are the most critical. Several decades of efforts devoted to the genetic improvement of maize have resulted in remarkable genetic gain, leading to increased yields of maize on farmers’ fields. The revolution unfolding in the areas of genomics, bioinformatics, and phenomics is generating innovative tools, resources, and technologies for transforming crop breeding programs. It is envisaged that such tools will be integrated within maize breeding programs, thereby advancing these programs and addressing current and future challenges. Accordingly, the maize improvement program within International Institute of Tropical Agriculture (IITA) is undergoing a process of modernization through the introduction of innovative tools and new schemes that are expected to enhance genetic gains and impact on smallholder farmers in the region. Genomic tools enable genetic dissections of complex traits and promote an understanding of the physiological basis of key agronomic and nutritional quality traits. Marker-aided selection and genome-wide selection schemes are being implemented to accelerate genetic gain relating to yield, resilience, and nutritional quality. Therefore, strategies that effectively combine genotypic information with data from field phenotyping and laboratory-based analysis are currently being optimized. Molecular breeding, guided by methodically defined product profiles tailored to different agroecological zones and conditions of climate change, supported by state-of-the-art decision-making tools, is pivotal for the advancement of modern, genomics-aided maize improvement programs. Accelerated genetic gain, in turn, catalyzes a faster variety replacement rate. It is critical to forge and strengthen partnerships for enhancing the impacts of breeding products on farmers’ livelihood. IITA has well-established channels for delivering its research products/technologies to partner organizations for further testing, multiplication, and dissemination across various countries within the subregion. Capacity building of national agricultural research system (NARS) will facilitate the smooth transfer of technologies and best practices from IITA and its partners

Leveraging agrigenomics" for crop improvement"

Modern biotechnologies have dramatically reshaped the crop improvement research during the past decade. Biotechniques have become indispensable for efficient and effective development of new knowledge, processes, and products. IITA's biotechnology, strategized as three major themes― genomics, transgenics, and diagnostics, is directed toward the genetic improvement of staple food crops of Africa, such as cooking-banana, plantain, cassava, yam, and cowpea. This section provides some insights and progress in this program

Genomics for transforming yam breeding

Yam (Dioscorea spp.), a multispecies, polyploidy, and vegetatively propagated crop, is an economically important staple food for more than 300 million people in West Africa, Asia, Oceania, and the Caribbean. The five major yam-producing countries in West Africa (Bénin, Côte d’Ivoire, Ghana, Nigeria, and Togo) account for 93% of worldwide production. Dioscorea rotundata and D. alata are the species most commonly cultivated in West Africa1. The genetic improvement of yam is faced with several constraints, including the long growth cycle (about 8 months or more), dioecy, plants that flower poorly or not at all, polyploidy, vegetative propagation, heterozygous genetic background, and poor knowledge about the genetics of the crop2

Isolation and characterization of resistant gene analogs in cassava, wild Manihot species, and castor bean (Ricinus communis)

Cassava, Manihot esculenta, is one of the major food crops in sub-Saharan Africa (SSA) providing the bulk of dietary calories to hundreds of millions of households. Two viral diseases, namely cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) pose a serious threat to cassava production. The emergence of new virus species and strains that overcome the existing resistant/tolerant cultivars entails identification and pyramiding of new sources of resistance using marker-aided selection. The isolation of resistance gene analogues (RGAs) using a homology-based approach can provide useful resources towards this goal. Degenerate primers based on the conserved motif of the nucleotide binding site (NBS) domain from resistance (R) genes were used to isolate RGAs from genomic DNA and cDNA in cassava, wild Manihot species, and castor bean (Ricinus communis). A total of 552 RGAs sequences were identified and deposited in GenBank. Conserved motifs such as P-loop, Kinase-2a and GLPL were present in the NBS domain. This study sheds light on the nature of NBS- leucine-rich repeat (LRR) R genes in cassava and closely related taxa in the family Euphorbiaceae. These candidate sequences mapped to the draft cassava genome with high sequence similarity to predicted NBS-LRR genes. These novel sequences may serve as a stepping stone for further characterization and experimental validation of predicted R genes in the draft cassava genome, ultimately leading to the development of functional gene-targeted markers that can be used in molecular resistance breeding aimed at combating CBSD and CMD

Quantitative trait loci mapping for resistance to maize streak virus in F2: 3 population of tropical maize

Open Access Article; Published online: 01 Feb 2020Maize streak virus (MSV) continues to be a major biotic constraint for maize production throughout Africa. Concerning the quantitative nature of inheritance of resistance to MSV disease (MSVD), we sought to identify new loci for MSV resistance in maize using F2:3 population. The mapping population was artificially inoculated with viruliferous leafhoppers under screenhouse and evaluated for MSVD resistance. Using 948 DArT markers, we identified 18 quantitative trait loci (QTLs) associated with different components of MSVD resistance accounting for 3.1–21.4% of the phenotypic variance, suggesting that a total of eleven genomic regions covering chromosomes 1, 2, 3, 4, 5 and 7 are probably required for MSVD resistance. Two new genomic regions on chromosome 4 revealed the occurrence of co-localized QTLs for different parameters associated with MSVD resistance. Moreover, the consistent appearance of QTL on chromosome 7 for MSVD resistance is illustrating the need for fine-mapping of this locus. In conclusion, these QTLs could provide additional source for breeders to develop MSV resistance

Markertrait association analysis of functional gene markers for provitamin A levels across diverse tropical yellow maize inbred lines

Background: Biofortification of staple crops is a cost effective and sustainable approach that can help combatvitamin A and other micronutrient deficiencies in developing countries. PCR -based DNA markers distinguishingalleles of three key genes of maize endosperm carotenoid biosynthesis (PSY1, lcyE and crtRB1) have been developedto facilitate maize provitamin A biofortification via marker assisted selection. Previous studies of these functionalDNA markers revealed inconsistent effects. The germplasm previously employed for discovering andvalidating these functional markers was mainly of temperate origin containing low frequencies of the favourableallele of the most significant polymorphism, crtRB1-5_TE. Here, we investigate the vitamin A biofortification potentialof these DNA markers in a germplasm panel of diverse tropical yellow maize inbred lines, with mixed geneticbackgrounds of temperate and tropical germplasm to identify the most effective diagnostic markers forvitamin A biofortification.Results: The functional DNA markers crtRB1-5_TE and crtRB1-3_TE were consistently and strongly associated withprovitamin A content across the tropical maize inbred lines tested. The alleles detected by these two functionalmarkers were in high linkage disequilibrium (R2 = 0.75) and occurred in relatively high frequency (18%). Genotypescombining the favourable alleles at the two loci (N = 20) displayed a 3.22 fold average increase in _-carotenecontent compared to those genotypes lacking the favourable alleles (N = 106). The PSY1 markers were monomorphicacross all of the inbred lines. The functional DNA markers for lcyE were associated with lutein, and with the ratio ofcarotenoids in the alpha and beta branches, but not with provitamin A levels. However, the combined effects of thetwo genes were stronger than their individual effects on all carotenoids.Conclusions: Tropical maize inbred lines harbouring the favourable alleles of the crtRB1-5_TE and 3_TE functionalmarkers produce higher levels of provitamin A. Such maize lines can be used as donor parents to speed up thedevelopment of provitamin A biofortified tropical maize varieties adapted to growing conditions and consumerpreferences, providing a route towards mitigation of vitamin A malnutrition in Sub-Saharan Africa

Cassava improvement in the era of "agrigenomics": the road to nextgeneration breeding.

In the last 45 years, IITA has played a pivotal role in the genetic improvement of cassava for resourcepoor farmers in sub-Saharan Africa (SSA). More than 400 varieties have been developed that are not only high yielding but also resistant to diseases and pests. Many of these improved varieties have been extensively deployed in SSA and have helped to avert humanitarian crises caused by the viral disease pandemics that devastated local landraces in East and Central Africa

Optimizing sample size for molecular characterization of open-pollinated maize (Zea mays L.) varieties using simple sequence repeat markers

Molecular-based characterization of open-pollinated varieties (OPVs) in maize is useful to define their unique profiles. A total of 58 SSR markers selected from a panel of 70 were used for genotyping three samples of 30, 50 and 100 plant bulks for each of 32 OPVs. The SSR markers detected a total of 253 alleles in the 32 maize OPVs across the three bulk samples. The number of alleles per marker varied from 2 to 7, with an overall mean of 4.36. The genetic distance among the OPVs varied from 0.17 to 0.93 with an average of 0.70 ± 0.007 for bulk samples of 30 plants, 0.20 to 0.91 with an overall mean of 0.70 ± 0.007 for bulk samples of 50 plants and from 0.30 to 0.95 with an average of 0.75 ± 0.006 for bulk samples of 100 plants. Cluster analysis separated the 32 maize OPVs into two major groups, which were further separated into two sub-groups for each type of bulk sample. The groupings of the OPVs into two major groups and their corresponding sub-groups was consistent with known breeding history (common parentage) and common target traits during development of the OPVs irrespective of the sample size used. However, in the bulk samples of 50 and 100 plants, some sub-groups were composed of OPVs with mixed maturity classes and diverse genetic backgrounds. Of the three independent bulk samples, the smallest sample size of 30 plants was found to be optimal for characterizing heterogeneous and heterozygous maize populations and OPVs owing to its cost-effectiveness and relative ease of sample processing

Field collection, preservation and large scale DNA extraction procedures for cassava (Manihot esculenta Crantz.)

Some genetic studies using molecular methods such as diversity assessment or marker-assisted selection require collection of a large number of samples from fields located in the vicinity or in remote areas, followed by isolation of good quality DNA in a short time span. In the present study, different tissue preservation methods were compared for subsequent DNA extraction using a modified CTAB method in two 96-well plates, following grinding of leaf tissues with a GenoGrinder 2000. We found that preservation of leaf tissues in NaCl-CTAB-azide buffer (as described in Rogstad, 1992) at 4°C is a better storage procedure than preservation at -20°C to obtain good quality DNA. Comparison of DNA extraction with or without use of phenol revealed that the quality of DNA was not drastically affected when non-phenol extraction protocol was used and did not affect PCR amplification. Thus, the recommended DNA extraction procedure allowed us to process 192 samples per day at a cost of $0.80 per sample, with an average yield of 1.8  g, suitable for both PCR and genotyping

Evaluating testcross performance and genetic divergence of lines derived from reciprocal tropical maize composites

The development of hybrids with enhanced expression of heterosis depends on the genetic background of the source population and the effectiveness of a breeding scheme used to identify and use divergent inbred lines with good combining ability. The present study was conducted to examine the potential of improved tropical reciprocal composites as sources of inbred lines for developing productive hybrids. Thirty-six S4 lines derived from the third RRS cycle of each composite were crossed in pairs to form 36 testcrosses, which were evaluated along with commonly grown commercial hybrids in Nigeria across nine test environments. Results showed consistent ranking of testcrosses for grain yield and other traits across the diverse test environments. The best 22 testcrosses produced 21% to 51% more grain yields than the highest yielding commercial hybrid. Several testcrosses combined high grain yields with other desirable agronomic traits. The SSR and SNP markers used in the present study detected a broad range of genetic diversity among the 72 S4 lines, which was structured along the two composites. The two markers portrayed similar trends in determining genetic distance estimates and detecting composite-specific alleles in the S4 lines. These results highlight the potential of improved reciprocal composites as sources of new and divergent parents for developing productive hybrids and as sources of novel alleles for broadening and diversifying the genetic base of adapted germplasm to sustain genetic gain in productivity of hybrids in WCA