Using an incomplete block design to allocate lines to environments improves sparse genome-based prediction in plant breeding

Osval Antonio Montesinos-Lopez ABELARDO MONTESINOS LOPEZ RICARDO ACOSTA DIAZ Rajeev Varshney Jose Crossa ALISON BENTLEY (2022, [Artículo])

Genomic selection (GS) is a predictive methodology that trains statistical machine-learning models with a reference population that is used to perform genome-enabled predictions of new lines. In plant breeding, it has the potential to increase the speed and reduce the cost of selection. However, to optimize resources, sparse testing methods have been proposed. A common approach is to guarantee a proportion of nonoverlapping and overlapping lines allocated randomly in locations, that is, lines appearing in some locations but not in all. In this study we propose using incomplete block designs (IBD), principally, for the allocation of lines to locations in such a way that not all lines are observed in all locations. We compare this allocation with a random allocation of lines to locations guaranteeing that the lines are allocated to

the same number of locations as under the IBD design. We implemented this benchmarking on several crop data sets under the Bayesian genomic best linear unbiased predictor (GBLUP) model, finding that allocation under the principle of IBD outperformed random allocation by between 1.4% and 26.5% across locations, traits, and data sets in terms of mean square error. Although a wide range of performance improvements were observed, our results provide evidence that using IBD for the allocation of lines to locations can help improve predictive performance compared with random allocation. This has the potential to be applied to large-scale plant breeding programs.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA Bayes Theorem Genome Inflammatory Bowel Diseases Models, Genetic Plant Breeding

EGS planning, production, maintenance of inbred lines and Quality Assurance/Quality Control (QA/QC)

Fidelis Owino Berhanu Tadesse Ertiro (2022, [Objeto de congreso])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA INBRED LINES SEED QUALITY QUALITY CONTROL GENETIC MARKERS

Preliminary dissection of grain yield and related traits at differential nitrogen levels in diverse pre-breeding wheat germplasm through association mapping

Achla Sharma Juan Burgueño Prashant Vikram Nitika Sandhu Satinder Kaur Parveen Chhuneja (2023, [Artículo])

Plant Nitrogen Use Efficiency Pre-Breeding Lines Genome-Wide Association Study Marker Trait Association CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA WHEAT PRE-BREEDING BREEDING LINES NITROGEN LANDRACES GENETIC MARKERS

Breeding for native genetic resistance to FAW in Africa-adapted early- and intermediate-maturing tropical maize germplasm

Yoseph Beyene Anani Bruce Manje Gowda Andrew Chavangi Prasanna Boddupalli (2023, [Objeto de congreso])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA BREEDING GENETIC RESISTANCE MAIZE GERMPLASM HYBRIDS

Chapter 9. Genome-informed discovery of genes and framework of functional genes in wheat

awais rasheed Rudi Appels (2024, [Capítulo de libro])

Wheat Genomics KASP Markers Gene Discovery Functional Markers Gene Networks CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA WHEAT GENOMICS SINGLE NUCLEOTIDE POLYMORPHISMS FUNCTIONAL GENOMICS

Molecular pre-breeding in wheat physiology

David González-Diéguez (2023, [Objeto de congreso])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA WHEAT PRE-BREEDING MOLECULAR GENETICS MARKER-ASSISTED SELECTION INTROGRESSION

Complex traits and candidate genes: estimation of genetic variance components across multiple genetic architectures

GIOVANNY COVARRUBIAS-PAZARAN Hans-Peter Piepho (2023, [Artículo])

Average Semivariance Linear Mixed Model Variance Component Estimation Polygenic Inheritance Oligogenic Inheritance Mendelian Inheritance CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA MENDELISM GENETIC VARIANCE GENOME-WIDE ASSOCIATION STUDIES PHENOTYPES CHROMOSOME MAPPING

Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society

Vanika Garg Rutwik Barmukh Manish Roorkiwal Chris Ojiewo Abhishek Bohra MAHENDAR THUDI Vikas Kumar Singh Himabindu Kudapa Reyaz Mir Chellapilla Bharadwaj Xin Liu Manish Pandey (2024, [Artículo])

Agricultural Biotechnology Crop Genomics Genome Sequencing CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA BIOTECHNOLOGY CROPS GENOMICS PLANT BREEDING AGRICULTURE GENETIC IMPROVEMENT

An efficient transformation method for genome editing of elite bread wheat cultivars

Akshaya Biswal Kanwarpal Dhugga (2023, [Artículo])

Particle Bombardment Wheat Growth-Regulating Factor 4 Wheat Growth-Interacting Factor Wheat Mildew Locus O CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CRISPR GENE EDITING TRANSFORMATION WHEAT

Transcriptome mining provides insights into cell wall metabolism and fiber lignification in Agave tequilana Weber

Luis Fernando Maceda Lopez ELSA BEATRIZ GONGORA CASTILLO Enrique Ibarra-Laclette DALIA C. MORAN VELAZQUEZ AMARANTA GIRON RAMIREZ Matthieu Bourdon José Luis Villalpando Aguilar Gabriela Chavez-Calvillo Toomer John Tang Parastoo Azadi Jorge Manuel Santamaría Fernández Itzel López-Rosas Mercedes G Lopez June Simpson FULGENCIO ALATORRE COBOS (2022, [Artículo])

Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioen-ergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for un-derstanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

AGAVE CELL WALLS LIGNOCELLULOSE CAD PROTEIN CESA PROTEIN SCLERENCHYMA BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA MOLECULAR DE PLANTAS GENÉTICA MOLECULAR DE PLANTAS