Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs.

Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.

A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits.

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs.

Substitution of Chemical Fertilizer with Organic Fertilizer Affects Soil Total Nitrogen and Its Fractions in Northern China.

The impact of chemical to organic fertilizer substitution on soil labile organic and stabilized N pools under intensive farming systems is unclear. Therefore, we analyzed the distribution of soil total N (STN), particulate organic N (PON), microbial biomass N (MBN), dissolved organic N (DON), and mineral N (NO and NH) levels down to 100 cm profile under wheat-maize rotation system in northern China. The experiment was established with four 270 kg ha N equivalent fertilizer treatments: Organic manure (OM); Organic manure with nitrogen fertilizer (OM + NF); Nitrogen fertilizer (NF); and Control (CK).

Machine Learning-Based Plant Detection Algorithms to Automate Counting Tasks Using 3D Canopy Scans.

This study tested whether machine learning (ML) methods can effectively separate individual plants from complex 3D canopy laser scans as a prerequisite to analyzing particular plant features. For this, we scanned mung bean and chickpea crops with PlantEye (R) laser scanners. Firstly, we segmented the crop canopies from the background in 3D space using the Region Growing Segmentation algorithm.

Understanding Heterosis, Genetic Effects, and Genome Wide Associations for Forage Quantity and Quality Traits in Multi-Cut Pearl Millet.

Pearl millet is an important food and fodder crop cultivated in the arid and semi-arid regions of Africa and Asia, and is now expanding to other regions for forage purpose. This study was conducted to better understand the forage quantity and quality traits to enhance the feed value of this crop. Two sets of pearl millet hybrids (80 single cross hybrids in Set-I and 50 top cross hybrids in Set-II) along with their parents evaluated multi-locationally for the forage-linked traits under multi-cut (two cuts) system revealed significant variability for the forage traits in the hybrids and parents.

Bayesian multitrait kernel methods improve multienvironment genome-based prediction.

When multitrait data are available, the preferred models are those that are able to account for correlations between phenotypic traits because when the degree of correlation is moderate or large, this increases the genomic prediction accuracy. For this reason, in this article, we explore Bayesian multitrait kernel methods for genomic prediction and we illustrate the power of these models with three-real datasets. The kernels under study were the linear, Gaussian, polynomial, and sigmoid kernels; they were compared with the conventional Ridge regression and GBLUP multitrait models.

Marker-assisted forward breeding to develop a drought-, bacterial-leaf-blight-, and blast-resistant rice cultivar.

Among the different challenges related to rice (Oryza sativa L.) cultivation, drought, bacterial leaf blight (BLB), and blast are the key stresses that significantly affect grain yield (GY) in rice. To ameliorate this issue, marker-assisted forward breeding (MAFB) coupled with a simultaneous crossing approach was used to combine three drought tolerant quantitative trait loci (QTL)-qDTY , qDTY , and qDTY -four BLB genes-Xa4, xa5, xa13, and Xa21-and one blast-resistance gene, Pi9, in the elite rice cultivar Lalat.

Metabolite Diversity and Metabolic Genome-Wide Marker Association Studies (Mgwas) for Health Benefiting Nutritional Traits in Pearl Millet Grains.

As efforts are made to increase food security, millets are gaining increasing importance due to their excellent nutritional credentials. Among the millets, pearl millet is the predominant species possessing several health benefiting nutritional traits in its grain that are helpful in mitigating chronic illnesses such as type-2 diabetes and obesity. In this paper, we conducted metabolomic fingerprinting of 197 pearl millet inbred lines drawn randomly from within the world collection of pearl millet germplasm and report the extent of genetic variation for health benefitting metabolites in these genotypes.

Characterization of rhizobia isolated from leguminous plants and their impact on the growth of ICCV 2 variety of chickpea ( L.).

Six rhizobia-like-bacterial strains in total, secluded from the root and stem nodules of various leguminous plants were characterized for growth promoting ability on ICCV 2 variety of chickpea. Bacterial strains showed production of IAA, NH, siderophore, HCN, ACC deaminase, hydrolytic enzyme production such as chitinase, amylase, protease, lipase, β-1, 3-glucanase and solubilization of nutrients such as phosphate, zinc and potassium. However the performance of PGP traits characterized varied among the six bacterial strains.

DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds.

The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential.

Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding.

Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons.

Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations.

Background: Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis.

Results: Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.

A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding.

Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing.

Genotyping-by-sequencing (GBS) has emerged as a cost-effective approach for genome-wide discovery of single-nucleotide polymorphism (SNP) markers and high-throughput genotyping. In this study, 96 coconut palms, representing 16 accessions from globally diverse origins, were genotyped using the GBS strategy. A total of 10,835 high-quality SNPs, which were identified after stringent filtering, were utilized to assess genetic diversity, population structure, and linkage disequilibrium (LD) analyses.

Generic algorithm for multicriteria ranking of crop technological options based on the "Technique for Order of Preference by Similarity to Ideal Solution" using ShinyApps.

Many agricultural research and development programs aiming at enhancing tradeoffs related to different adoption, management and policy decisions face a methodological problem in which multi-criteria ranking is used to reach acceptable compromises between different objectives (e.g. those of farms, research managers, donors or policy makers).

Features and applications of haplotypes in crop breeding.

Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications.

Next Generation dsRNA-Based Insect Control: Success So Far and Challenges.

RNA interference (RNAi) is a method of gene silencing where dsRNA is digested into small interfering RNA (siRNA) in the presence of enzymes. These siRNAs then target homologous mRNA sequences aided by the RNA-induced silencing complex (RISC). The mechanism of dsRNA uptake has been well studied and established across many living organisms including insects.

Millets Can Have a Major Impact on Improving Iron Status, Hemoglobin Level, and in Reducing Iron Deficiency Anemia-A Systematic Review and Meta-Analysis.

The prevalence of iron deficiency anemia is highest among low and middle-income countries. Millets, including sorghum, are a traditional staple in many of these countries and are known to be rich in iron. However, a wide variation in the iron composition of millets has been reported, which needs to be understood in consonance with its bioavailability and roles in reducing anemia.

Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa.

Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two-stage analysis.

Genome-Wide Association Mapping Identifies Novel Panicle Morphology Loci and Candidate Genes in Sorghum.

Panicle morphology is an important trait in racial classification and can determine grain yield and other agronomic traits in sorghum. In this study, we performed association mapping of panicle length, panicle width, panicle compactness, and peduncle recurving in the sorghum mini core panel measured in multiple environments with 6,094,317 single nucleotide polymorphism (SNP) markers. We mapped one locus each on chromosomes 7 and 9 to recurving peduncles and eight loci for panicle length, panicle width, and panicle compactness.

Evaluation of Soybean Entries in the Pan-African Trials for Response to the Cause of Red Leaf Blotch.

Red leaf blotch (RLB), caused by the fungus , is an important disease of soybean known to cause yield losses across soybean-growing regions in Africa. Fungicides are one option to manage this disease, but utilization of host resistance may be a better option suited for smallholder soybean farmers in Africa. Fifty-nine soybean entries were evaluated for RLB severity in nine field locations in Ethiopia, Kenya, Uganda, and Zambia.

The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data.

QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in diverse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.

Identification of High-Yielding Iron-Biofortified Open-Pollinated Varieties of Pearl Millet in West Africa.

Pearl millet is a predominant food and fodder crop in West Africa. This study was carried out to test the newly developed open-pollinated varieties (OPVs) for field performance and stability for grain yield, grain iron (Fe), and grain zinc (Zn) contents across 10 locations in West Africa (i.e.