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      The double round-robin population unravels the genetic architecture of grain size in barley

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          Abstract

          Grain number, size and weight primarily determine the yield of barley. Although the genes regulating grain number are well studied in barley, the genetic loci and the causal gene for sink capacity are poorly understood. Therefore, the primary objective of our work was to dissect the genetic architecture of grain size and weight in barley. We used a multi-parent population developed from a genetic cross between 23 diverse barley inbreds in a double round-robin design. Seed size-related parameters such as grain length, grain width, grain area and thousand-grain weight were evaluated in the HvDRR population comprising 45 recombinant inbred line sub-populations. We found significant genotypic variation for all seed size characteristics, and observed 84% or higher heritability across four environments. The quantitative trait locus (QTL) detection results indicate that the genetic architecture of grain size is more complex than previously reported. In addition, both cultivars and landraces contributed positive alleles at grain size QTLs. Candidate genes identified using genome-wide variant calling data for all parental inbred lines indicated overlapping and potential novel regulators of grain size in cereals. Furthermore, our results indicated that sink capacity was the primary determinant of grain weight in barley.

          Abstract

          Multi-parent population has uncovered a natural allelic series across quantitative trait loci associated with grain size and weight that will contribute to identifying causal genes and yield improvement in barley.

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          Efficient methods to compute genomic predictions.

          Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and to estimate thousands of marker effects simultaneously. Algorithms were derived and computer programs tested with simulated data for 2,967 bulls and 50,000 markers distributed randomly across 30 chromosomes. Estimation of genomic inbreeding coefficients required accurate estimates of allele frequencies in the base population. Linear model predictions of breeding values were computed by 3 equivalent methods: 1) iteration for individual allele effects followed by summation across loci to obtain estimated breeding values, 2) selection index including a genomic relationship matrix, and 3) mixed model equations including the inverse of genomic relationships. A blend of first- and second-order Jacobi iteration using 2 separate relaxation factors converged well for allele frequencies and effects. Reliability of predicted net merit for young bulls was 63% compared with 32% using the traditional relationship matrix. Nonlinear predictions were also computed using iteration on data and nonlinear regression on marker deviations; an additional (about 3%) gain in reliability for young bulls increased average reliability to 66%. Computing times increased linearly with number of genotypes. Estimation of allele frequencies required 2 processor days, and genomic predictions required <1 d per trait, and traits were processed in parallel. Information from genotyping was equivalent to about 20 daughters with phenotypic records. Actual gains may differ because the simulation did not account for linkage disequilibrium in the base population or selection in subsequent generations.
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            R: a Language and Environment for StatisticalComputing

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              A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.

              Grain weight is one of the most important components of grain yield and is controlled by quantitative trait loci (QTLs) derived from natural variations in crops. However, the molecular roles of QTLs in the regulation of grain weight have not been fully elucidated. Here, we report the cloning and characterization of GW2, a new QTL that controls rice grain width and weight. Our data show that GW2 encodes a previously unknown RING-type protein with E3 ubiquitin ligase activity, which is known to function in the degradation by the ubiquitin-proteasome pathway. Loss of GW2 function increased cell numbers, resulting in a larger (wider) spikelet hull, and it accelerated the grain milk filling rate, resulting in enhanced grain width, weight and yield. Our results suggest that GW2 negatively regulates cell division by targeting its substrate(s) to proteasomes for regulated proteolysis. The functional characterization of GW2 provides insight into the mechanism of seed development and is a potential tool for improving grain yield in crops.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                J Exp Bot
                J Exp Bot
                exbotj
                Journal of Experimental Botany
                Oxford University Press (UK )
                0022-0957
                1460-2431
                08 December 2022
                12 September 2022
                12 September 2022
                : 73
                : 22
                : 7344-7361
                Affiliations
                Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University , Dusseldorf, Germany
                Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University , Dusseldorf, Germany
                Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University , Dusseldorf, Germany
                Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University , Dusseldorf, Germany
                Max Planck Institute for Plant Breeding Research , Cologne, Germany
                Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University , Dusseldorf, Germany
                Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University , Dusseldorf, Germany
                Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University , Dusseldorf, Germany
                Max Planck Institute for Plant Breeding Research , Cologne, Germany
                Cluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, Heinrich Heine University , Dusseldorf, Germany
                CIMMYT , Mexico
                Author notes
                Author information
                https://orcid.org/0000-0003-4878-6965
                https://orcid.org/0000-0001-6000-065X
                https://orcid.org/0000-0001-6791-8068
                Article
                erac369
                10.1093/jxb/erac369
                9730814
                36094852
                7da4e1a6-3859-439f-9387-5b41d958e042
                © The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 27 April 2022
                : 08 September 2022
                : 08 September 2022
                : 04 November 2022
                Page count
                Pages: 18
                Funding
                Funded by: Deutsche Forschungsgemeinschaft, DOI 10.13039/501100001659;
                Funded by: International Research Training Group;
                Award ID: 2466
                Award ID: 391465903
                Categories
                Research Papers
                Growth and Development
                AcademicSubjects/SCI01210

                Plant science & Botany
                barley,grain size,grain weight,multi-parent population,quantitative trait locus (qtl),yield-related traits

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