Heterosis and Heterotic Grouping among Tropical Maize Germplasm

Maize (Zea mays L.) is the most important staple cereal cultivated in sub-Saharan Africa but its productivity is considerable low due to several factors. Development and deployment of maize hybrids have been reported as one of the crucial options in achieving sustainable maize production in sub-Saharan Africa. Information on the heterotic response among available genetic materials in a breeding program is valuable before commencement of any hybrid development program. Unlike the temperate germplasm, maize tropical germplasm is characterized with wide genetic base and genetic complexities and thus, proper organization of the pools, populations, varieties and inbreds that can serve as parental materials for hybrid development through identification of a distinct heterotic groups and patterns among tropical germplasm becomes very essential. This paper reviewed past research efforts at characterizing heterotic response among tropical maize genetic materials with a view to point out merits and demerits in the methods used and future direction towards achieving sustainable hybrid cultivation and enhancing food security in the sub-region.

Validation of Functional Polymorphisms Affecting Maize Plant Height by Unoccupied Aerial Systems (UAS) Discovers Novel Temporal Phenotypes

Plant height (PHT) in maize (Zea mays L.) has been scrutinized genetically and phenotypically due to relationship with other agronomically valuable traits (e.g. yield). Heritable variation of PHT is determined by many discovered quantitative trait loci (QTLs); however, phenotypic effects of such loci often lack validation across environments and genetic backgrounds, especially in the hybrid state grown by farmers rather than the inbred state more often used by geneticists. A previous genome wide association study using a topcrossed hybrid diversity panel identified two novel quantitative trait variants (QTVs) controlling both PHT and grain yield. Here, heterogeneous inbred families demonstrated that these two loci, characterized by two single nucleotide polymorphisms (SNPs), cause phenotypic variation in inbred lines, but that size of these effects were variable across four different genetic backgrounds, ranging from 1 to 10 cm. Weekly unoccupied aerial system flights demonstrated the two SNPs had larger effects, varying from 10 to 25 cm, in early growth while effects decreased towards the end of the season. These results show that allelic effect sizes of economically valuable loci are both dynamic in temporal growth and dynamic across genetic backgrounds, resulting in informative phenotypic variability overlooked following traditional phenotyping methods. Public genotyping data shows recent favorable allele selection in elite temperate germplasm with little change across tropical backgrounds. As these loci remain rarer in tropical germplasm, with effects most visible early in growth, they are useful for breeding and selection to expand the genetic basis of maize.

Validation of Functional Polymorphisms Affecting Maize Plant Height by Unoccupied Aerial Systems (UAS) allows Novel Temporal Phenotypes

Plant height (PHT) in maize (Zea mays L.) has been scrutinized genetically and phenotypically due to relationship with other agronomically valuable traits (e.g. yield). Heritable variation of PHT is determined by many discovered quantitative trait loci (QTLs); however, phenotypic effects of such loci often lack validation across environments and genetic backgrounds, especially in the hybrid state grown by farmers rather than the inbred state preferred by geneticists. A previous genome wide association study using a hybrid diversity panel identified two novel quantitative trait variants (QTVs) controlling both PHT and grain yield. Here, heterogeneous inbred families demonstrated that these two loci, characterized by two single nucleotide polymorphisms (SNPs), cause phenotypic variation in inbred lines, but that size of these effects were variable across four different genetic backgrounds, ranging from 1 to 10 cm. Weekly unoccupied aerial system flights demonstrated both SNPs had larger effects, varying from 10 to 25 cm, in early growth while SNPs effects decreased towards the end of the season. These results show that allelic effect sizes of economically valuable loci are both dynamic in temporal growth and dynamic across genetic backgrounds resulting in informative phenotypic variability overlooked following traditional phenotyping methods. Public genotyping data shows recent favorably selection in elite temperate germplasm with little change across tropical backgrounds. As these loci remain rare in tropical germplasm, with effects most visible early in growth, they are useful for breeding and selection to expand the genetic basis of maize.

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

As a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies that capture substantial levels of both tropical and temperate diversity. We generated a pangenome representation (the Practical Haplotype Graph, PHG) of these assemblies in a database, representing the pangenome haplotype diversity and providing an initial estimate of structural diversity. We leveraged the pangenome to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS. We imputed the genotypes of the recombinant inbred lines of the NAM population with over 99% mean accuracy, while unrelated germplasm attained a mean imputation accuracy of 92 or 95% when using GBS or WGS data, respectively. Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database. Also, the PHG stores the imputation data in a 30,000-fold more space-efficient manner than a standard genotype file, which is a key improvement when dealing with large scale data.

Genetic diversity of maize landraces from the South-West of France

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France, a traditional region for maize cultivation. A set of landraces were collected in this region between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces fo this region showed that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridization between Caribbean and Northern Flint germplasms introduced in Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows, rather than through differential climatic adaptation. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found only few significant cases of hybridization between Caribbean and Northern Flint germplasms in the region. We also found gene flows from various maize genetic groups to SWF landraces. Thus, we assumed that SWF landraces had a multiple origin with a slightly higher influence of Tropical germplasm in the West and preponderance of Northern Flint germplasm in the East.

Effects of planting density and nitrogen fertilization level on grain yield and harvest index in seven modern tropical maize hybrids (Zea maysL.)

SUMMARYTo support tropical maize (Zea maysL.) breeding efforts, the current work aimed to assess harvest index (HI) in modern hybrids and determine the effect of different planting densities on grain yield and HI under well-fertilized (HN) and nitrogen (N) deficient conditions. Harvest index and grain yield of 34 hybrids on average reached 0·42 and 7·06 t/ha (five environments), indicating a large potential for improvement in HI relative to temperate hybrids. Ear weight (r= 0·88), HI (r= 0·78) and shoot dry weight (r= 0·68) were strongly associated with grain yield. In the second experiment, seven hybrids were evaluated at planting densities of 5, 7, 9 and 11 plants/m2under HN (six environments) and N deficient (LN) conditions (four environments) to assess the effect of planting density on grain yield and HI. Grain yield increased by 40·4 and 21·8% under HN and LN conditions when planting density was increased relative to the lowest planting density. Harvest index increased from 0·42 at 5 plants/m2to 0·45 at 11 plants/m2under HN conditions and decreased from 0·44 at 5 plants/m2to 0·42 at 9 plants/m2under LN conditions. Harvest index was maximized at planting densities of 8·33 plants/m2and 5·30 plants/m2under HN and LN conditions, respectively, while grain yield was maximized at 9·93 plants/m2and 7·89/m2. Optimal planting density maximizing both HI and grain yield were higher than planting densities currently used in tropical germplasm. It can be concluded that productivity in tropical maize could be increased both under intensive (+40·4%) and lower-input management (+21·8%) by increasing planting densities above those currently used in smallholder agriculture in Latin America and Sub-Saharan Africa, in environments targeted by the International Maize and Wheat Improvement Center.