Genome scan of Kenyan Themeda triandra populations by AFLP markers reveals a complex genetic structure and hints for ongoing environmental selection

Abstract Tropical and subtropical rangeland systems provide core ecosystem services for the welfare of human populations that rely on readiness and quality of forage resources. However, forage species are still widely overlooked by molecular biology studies. In the present study, we employ 366 AFLP markers to provide the first description of the genetic landscape of three Kenyan populations of Themeda triandra Forssk., a key wild grass forage species. By including Australian T. triandra accessions and other closely related species in a molecular phylogeny, we provide a first evaluation of the relationships existing between African and Australian germplasm. Genetic diversity, population genetic structure and recombination rates in Kenyan T. triandra populations were investigated in detail. GPS coordinates of each sampled population were used to retrieve meteorological data at specific locations, and environmental factors likely contributing to T. triandra genetic differentiation were taken into consideration using a correlative approach based on outlier loci distribution. The use of molecular markers unveiled some previously unknown aspects about the biology of T. triandra , namely: i) African and Australian T. triandra genotypes analyzed in this study are genetically undistinguishable, ii) sexual recombination of Kenyan T. triandra is likely to play a major role in its reproduction, and iii) environmental characteristics of the collection sites are correlated with the allelic distribution of a limited set of loci under selection

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

Background: To sustain the global requirements for food and renewable resources, unraveling the molecular networks underlying plant growth is becoming pivotal. Although several approaches to identify genes and networks involved in final organ size have been proven successful, our understanding remains fragmentary. Results: Here, we assessed variation in 103 lines of the Zea mays B73xH99 RIL population for a set of final leaf size and whole shoot traits at the seedling stage, complemented with measurements capturing growth dynamics, and cellular measurements. Most traits correlated well with the size of the division zone, implying that the molecular basis of final leaf size is already defined in dividing cells of growing leaves. Therefore, we searched for association between the transcriptional variation in dividing cells of the growing leaf and final leaf size and seedling biomass, allowing us to identify genes and processes correlated with the specific traits. A number of these genes have a known function in leaf development. Additionally, we illustrated that two independent mechanisms contribute to final leaf size, maximal growth rate and the duration of growth. Conclusions: Untangling complex traits such as leaf size by applying in-depth phenotyping allows us to define the relative contributions of the components and their mutual associations, facilitating dissection of the biological processes and regulatory networks underneath

Atmospheric drivers affect crop yields in Mozambique

Climate change has been inducing variations in the statistics of both the large-scale weather patterns and the local weather in many regions of the world, and these variations have been affecting several human activities, including agriculture. In this study, we look at the links between large-scale weather patterns and local weather as well as agriculture, with a specific regional focus on Mozambique between 1981 and 2019. First, we investigated linear trends and links between large-scale weather patterns and local weather in the region using the ERA5 dataset. We used the same data to investigate how climate change has been affecting the statistics of large-scale weather patterns. Then, we derived Mozambique country-level cereal yield data from FAO and linked it up with climate and weather data to assess what is the relationship between large-scale patterns and local agronomic outputs using a multiple linear regression (MLR) model with crop yield as the response variable and climate drivers as predictors. The results indicate that in Mozambique, the crop season warmed substantially and consistently with climate change-induced global warming, and the rainy season had become drier and shorter, with precipitation concentrated in fewer, more intense events. These changes in the local weather have been linked to variations in the statistics of large-scale weather patterns that characterize the (large-scale) atmospheric flow over the region. Our results indicate a negative impact on yield associated with climate change, with average yield losses of 20% for rice and 8% for maize over the analyzed period (1981–2019). This negative impact suggests that, at the country scale, further future warming during the growing season may offset some of the cereal yield gains from technological advances

Genome wide association study of agronomic and seed traits in a world collection of proso millet (Panicum miliaceum L.)

The climate crisis threatens sustainability of crop production worldwide. Crop diversification may enhance food security while reducing the negative impacts of climate change. Proso millet (Panicum milaceum L.) is a minor cereal crop which holds potential for diversification and adaptation to different environmental conditions. In this study, we assembled a world collection of proso millet consisting of 88 varieties and landraces to investigate its genomic and phenotypic diversity for seed traits, and to identify marker-trait associations (MTA)

Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence

Flooding events caused by severe rains and poor soil drainage can interfere with plant germination and seedling establishment. Rice is one of the cereal crops that has unique germination strategies under flooding. One of these strategies is based on the fast coleoptile elongation in order to reach the water surface and re-establish the contact with the air. Microorganisms can contribute to plant health via plant growth promoters and provide protection from abiotic stresses. To characterise the community composition of the microbiome in rice germination under submergence, a 16S rRNA gene profiling metagenomic analysis was performed of temperate japonica rice varieties Arborio and Lamone seedlings, which showed contrasting responses in terms of coleoptile length when submerged. This analysis showed a distinct microbiota composition of Arborio seeds under submergence, which are characterised by the development of a long coleoptile. To examine the potential function of microbial communities under submergence, culturable bacteria were isolated, identified and tested for plant growth-promoting activities. A subgroup of isolated bacteria showed the capacity to hydrolyse starch and produce indole-related compounds under hypoxia. Selected bacteria were inoculated in seeds to evaluate their effect on rice under submergence, showing a response that is dependent on the rice genotype. Our findings suggest that endophytic bacteria possess plant growth-promoting activities that can substantially contribute to rice seedling establishment under submergence

Combined large-scale phenotyping and transcriptomics in maize reveals a robust growth regulatory network

Leaves are vital organs for biomass and seed production because of their role in the generation of metabolic energy and organic compounds. A better understanding of the molecular networks underlying leaf development is crucial to sustain global requirements for food and renewable energy. Here, we combined transcriptome profiling of proliferative leaf tissue with indepth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations. Previously, correlation analysis in a classical biparental mapping population identified 1,740 genes correlated with at least one of 14 traits. Here, we extended these results with data from a multiparent advanced generation intercross population. As expected, the phenotypic variability was found to be larger in the latter population than in the biparental population, although general conclusions on the correlations among the traits are comparable. Data integration from the two diverse populations allowed us to identify a set of 226 genes that are robustly associated with diverse leaf traits. This set of genes is enriched for transcriptional regulators and genes involved in protein synthesis and cell wall metabolism. In order to investigate the molecular network context of the candidate gene set, we integrated our data with publicly available functional genomics data and identified a growth regulatory network of 185 genes. Our results illustrate the power of combining in-depth phenotyping with transcriptomics in mapping populations to dissect the genetic control of complex traits and present a set of candidate genes for use in biomass improvement

Multivariate analysis in the dissection of phenotypic variation of Ethiopian cultivated barley (Hordeum vulgare ssp Vulgare L.) genotypes

Efficient conservation and subsequent utilization of genetic resources are primarily dependent on the strength in the assessment of variation among geno-types. An experiment was carried out aiming at determining the extent of pheno-typic variability present in a panel of 320 barley genotypes and identifying candidate lines for further evaluation in improvement programs and successive utilization. It was conducted at two locations in Ethiopia, Aris Negelle and Holetta in the 2017/18 and 2018/19 cropping seasons. Among the best 30 lines for grain yield across all the environments, lines from farmers’ varieties constitute 73% and lines that mature in less than 85 days were identified. Based on the spike row number, the best-performing lines combined across all the environments were six-rowed types. Based on the two years’ data at Arsi Negelle the two-rowed spike type dominates, and at Holetta the six-rowed type. After principal component analysis, the first three PCs with an eigenvalue greater than one explained 70% of the variation. The correlation coefficient between grain and biomass yield was signifi-cant and though low (r = 0.38***). Significant, high, and negative correlation coef-ficient (−0.72***) was observed between 1000 kernel weight and the number of seeds per spike. A positive correlation between biomass and grain yield attracts farmers as a feed and food crop as it has also been signified in the current research. Having the improved barley gene pool largely from international sources, combining the improved materials with farmers’ varieties may minimize the existing gap between the local and improved barley gene pool

Data-driven, participatory characterization of farmer varieties discloses teff breeding potential under current and future climates

In smallholder farming systems, traditional farmer varieties of neglected and underutilized species (NUS) support the livelihoods of millions of growers and consumers. NUS combine cultural and agronomic value with local adaptation, and transdisciplinary methods are needed to fully evaluate their breeding potential. Here, we assembled and characterized the genetic diversity of a representative collection of 366 Ethiopian teff (Eragrostis tef) farmer varieties and breeding materials, describing their phylogenetic relations and local adaptation on the Ethiopian landscape. We phenotyped the collection for its agronomic performance, involving local teff farmers in a participatory variety evaluation. Our analyses revealed environmental patterns of teff genetic diversity and allowed us to identify 10 genetic clusters associated with climate variation and with uneven spatial distribution. A genome-wide association study was used to identify loci and candidate genes related to phenology, yield, local adaptation, and farmers' appreciation. The estimated teff genomic offset under climate change scenarios highlighted an area around lake Tana where teff cropping may be most vulnerable to climate change. Our results show that transdisciplinary approaches may efficiently propel untapped NUS farmer varieties into modern breeding to foster more resilient and sustainable cropping systems

TRANSCRIPTIONAL ANALYSIS OF EIGHT MAGIC MAIZE PARENTAL LINES INFECTED WITH FUSARIUM VERTICILLIOIDES

Maize (Zea mays L.) is among the most important crops worldwide for food, feed, biofuels, and industrial applications. Its cultivation faces significant constraints due to Fusarium species that affect the quality and quantity of maize products. Among these, Fusarium verticillioides is responsible for severe diseases including seedling blights, stalk rot, and ear rot. The impact of the fungus is worsened by the fact that chemical and agronomic measures used to control Fusarium infection are often inefficient. Hence, genetic resistance is considered the most reliable resource to reduce damages caused by F. verticillioides. This study aims to elucidate the genetic basis of resistance to this fungus in maize. Young seedlings of eight divergent maize lines, founder of the MAGIC population, were artificially inoculated with a F. verticillioides strain using the rolled towel assay method. Total RNA was extracted from both control and treated samples after 72 hours of artificial inoculation and underwent paired-end sequenced with Illumina technology. Here we report the use this large transcriptomic dataset to identify the early transcriptional changes and the differentially expressed genes (DEGs) involved in fungal infection. The analysis identified several hundred DEGs, whose functions were explored through Gene Ontology enrichment analysis. A co-expression network analysis further refined the set of genes with potential implications in disease response. The results identify a limited set of genes that might play an important roles in maize resistance to F. verticillioides providing new insights into the molecular resistance mechanisms against the pathogen

CHARACTERIZING HETEROSIS IN A SET OF RECOMBINANT INTERCROSSES (RIXS) DEVELOPED FROM A MULTIPARENTAL MAIZE POPULATION

The exploitation of heterosis is key in modern maize breeding to capture the superior performance of heterozygous genotypes. Here, we developed a recombinant intercross (RIX) population in maize by crossing pairs of multiparental MAGIC recombinant inbred lines (RILs) to evaluate the heterosis across mosaics of eight maize haplotypes. Field phenotyping was performed on 400 RIX genotypes considering 11 agronomic traits as well as the resistance to Fusarium Ear Rot (FER), caused by Fusarium verticillioides (Sacc.) Nirenberg, in 2018 and 2019 in Piacenza, northern Italy. Phenotypic data showed a broad range of diversity in production and phenology traits thanks to the high level of allelic diversity available in parental genomes. The heterotic response of agronomic traits was computed based on RIL values as mid parent heterosis (MPH) and best parent heterosis (BPH). Both heterosis measures showed different magnitudes for different traits, with higher level of heterosis in yield and lower in flowering time, suggesting effects from partial dominance to over-dominance. No correlation was observed between phenotypic performance and heterozygosity level of RIXs for most of the agronomic traits. A preliminary quantitative trait locus (QTL) mapping detected a number of significant associations with agronomic traits across all chromosomes. The RIX collection showed a moderate heritability of FER resistance, and QTL were associated to this trait as well. The allelic effect estimates by our mapping model indicated the presence of minor effect QTL with relatively small additive effects on disease resistance in both years. Our findings confirm the usefulness of the RIX population to decipher heterotic loci in maize and support utilizing this resource in future to accelerate crop improvement