S McCouch

In this study, we model and predict rice yields by integrating molecular marker variation, varietal productivity, and climate, focusing on the Southern U.S. rice-growing region. This region spans the states of Arkansas, Louisiana, Texas, Mississippi, and Missouri and accounts for 85% of total U.S. rice production. By digitizing and combining four decades of county-level variety acreage data (1970 to 2015) with varietal information from genotyping-by-sequencing data, we estimate annual historical county-level allele frequencies. These allele frequencies are used together with county-level weather and yield data to develop ten machine learning models for yield prediction. A two-layer meta-learner ensemble model that combines all ten methods is externally evaluated against observations from historical Uniform Regional Rice Nursery trials (1980 to 2018) conducted in the same states. Finally, the ensemble model is …

Genomic selection (GS) has revolutionized breeding practices by integrating genotype and phenotype data to predict genomic estimated breeding values (GEBVs), offering the potential to accelerate breeding cycles and intensify and enhance early-stage selections. This approach relies on the concept of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) within populations. LD is the non-random association between alleles at different loci and provides valuable insights into recombination rates. This study aimed to investigate the influence of recombination on haplotype sizes and LD, assess the impact of additive (A) versus additive+ epistasis (A+ I) genetic models on GS prediction accuracy, and demonstrate how haplotype resolution in the training set (TS) impacts the prediction accuracy of GS. For this, we used biparental (MP2) and multiparent (MP6-8) populations, where the only difference between them was the recombination rate. Results revealed a direct relationship between LD decay and the number of recombination opportunities within populations, with smaller haplotype blocks observed in populations experiencing more recombination. The use of A+ I models increased heritability but did not improve prediction accuracy. Finally, populations with smaller haplotype sizes in the TS exhibited enhanced prediction accuracy. This study demonstrates the effect of haplotype size on GS accuracy, and its uniqueness lies in its focus on populations where the sole differentiating factor is haplotype size. It offers an important tool for breeders in designing GS strategies, providing valuable guidance for future …

MS Swaminathan, a visionary and inspiring leader, was born in Kumbakonam, Tamil Nadu, India, on August 7, 1925. He received his early education at the Catholic Little Flower High School in Kumbakonam, where he matriculated at the age of 15. He pursued his undergraduate degree in Zoology at Maharaja’s College in Trivandrum, Kerala, and obtained a Bachelor of Science degree in agriculture from Tamil Nadu Agricultural University, Coimbatore, in 1944. Subsequently, in 1947, he joined the Indian Agricultural Research Institute (IARI) in New Delhi and earned a postgraduate (Master of Science) degree in cytogenetics in 1948. Swaminathan was also a United Nations Educational, Scientific and Cultural Organization (UNESCO) fellow at Wageningen Agricultural University in the Netherlands for eight months. In 1950, he joined the plant breeding institute at the Cambridge School of Agriculture and completed …

Agriculture relies on plant breeding and genetics to deliver the best crop varieties and agronomic practices that will deploy results across nearly a billion hectares of cropland. We regularly see industry delivering on this objective, although optimized for their goals and limited geographies. However, many public sector efforts responsible for feeding most of the planet are not meeting these objectives or working effectively across disciplines. A key example is repeated publications on single genes, multiple gene constructs, or similar edits that claim to confer incredible yield increases. Many of these publications are flawed in how they measure and report yield. Often, they lack replication across environments, have low sample sizes, compare yield estimates in non-commercially competitive germplasm, and report on experiment-specific yields that massively underperform as compared to real-world local or global yields. Here, we detail common issues that arise and describe how such findings, when published in high-profile journals, skew global agricultural funding away from proven plant breeding methods. To address these issues, we suggest approaches for researchers and reviewers to use when evaluating the impact of single genes on crop yield, including: Robustly measure crop-relevant yield, not plant-level yield. Create field designs that pay attention to inter-plant competition and genotype-by-environment interactions. Use elite germplasm. Prioritize genes that evolution may have missed or whose variation has been exhausted within elite germplasm. Develop collaborations and use public sector frameworks such as the Genome to Fields …

Root anatomical traits show significant variation among rice, Oryza sativa L., genotypes and are of interest for improving adaptation to a variety of edaphic, hydrological and nutritional environments in which rice is grown. However, they are difficult to measure and the genetic controls of these traits are not well understood in rice. We conducted genome-wide association (GWA) analyses using moderate- and high-density SNP panels on a diverse rice population to identify genomic regions and candidate genes that control root anatomical traits. We identified 28 genomic regions for metaxylem vessel area and number, root cross-sectional area, stele area, and aerenchyma area. One genomic region associated with metaxylem vessel number and two regions associated with three root thickness-related traits, stele area, root cross-sectional area and metaxylem vessel area, were supported by chromosome-specific GWA using a high-density SNP panel and are regarded as highly significant regions controlling trait variation. Candidate genes in these regions were related to cell differentiation, elongation and division, and secondary cell wall formation. For genomic regions identified in the indica subpopulation, haplotype variation and root anatomical phenotypes were associated with geographic distributions of the accessions, notably the presence of alternate alleles conferring larger diameter roots, stele, and metaxylem vessels in accessions from the indica 2 and indica 3 subgroups originating largely in south and southeast Asia. The identification of genomic regions and candidate genes related to root anatomical traits in a diverse panel of rice …

This information session will showcase the latest thinking from CGIAR and the Crop Trust about how the genetic diversity of crops conserved in genebanks can be used for the benefit of smallholder farmers the world over.

Passport data (basic information about an accession, e.g., information about the crop classification, collecting site, existence of specimens and images, availability), phenotypic data, seed stock regeneration and requests for germplasm are among many data that require management within and among genebanks. Platforms such as Germinate, Legume Information system and BRIDGE address this requirement by providing access to 286detailed experimental and trial data on subsets of germplasm, which may or may not be held within the genebank system. The open-access platforms GRIN-Global, EURISCO and Genesys form the key components that provide central on-line searchable databases on material held in genebanks. Portals and databases that are providing an interface to PGR collections have issues and complexities that arise from the introduction of current omics data and bring up challenges and …

Two species of rice have been independently domesticated from different ancestral wild species in Asia and Africa. Comparison of mutations that underlie phenotypic and physiological alterations associated with domestication traits in these species gives insights into the domestication history of rice in both regions. Asian cultivated rice, Oryza sativa, and African cultivated rice, Oryza glaberrima, have been modified and improved for common traits beneficial for humans, including erect plant architecture, nonshattering seeds, nonpigmented pericarp, and lack of awns. Independent mutations in orthologous genes associated with these traits have been documented in the two cultivated species. Contrary to this prevailing model, selection for awnlessness targeted different genes in O. sativa and O. glaberrima. We identify Regulator of Awn Elongation 3 (RAE3) a gene that encodes an E3 ubiquitin ligase and is …