Browsing by Subject "Plant breeding"

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    Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing
    (Springer Nature, 2021-02-08) Valliyodan, Babu; Brown, Anne V.; Wang, Juexin; Patil, Gunvant; Liu, Yang; Otyama, Paul I.; Nelson, Rex T.; Vuong, Tri; Song, Qijian; Musket, Theresa A.; Wagner, Ruth; Marri, Pradeep; Reddy, Sam; Sessions, Allen; Wu, Xiaolei; Grant, David; Bayer, Philipp E.; Roorkiwal, Manish; Varshney, Rajeev K.; Liu, Xin; Edwards, David; Xu, Dong; Joshi, Trupti; Cannon, Steven B.; Nguyen, Henry T .; Biomedical Engineering and Informatics, Luddy School of Informatics, Computing, and Engineering
    We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.
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    Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years
    (Springer, 2023-07-21) Wonneberger, Ronja; Schreiber, Miriam; Haaning, Allison; Muehlbauer, Gary J.; Waugh, Robbie; Stein, Nils; Pediatrics, School of Medicine
    Selection over 70 years has led to almost complete fixation of a haplotype spanning ~ 250 Mbp of chomosome 5H in European two-rowed spring barleys, possibly originating from North Africa. Plant breeding and selection have shaped the genetic composition of modern crops over the past decades and centuries and have led to great improvements in agronomic and quality traits. Knowledge of the genetic composition of breeding germplasm is essential to make informed decisions in breeding programs. In this study, we characterized the structure and composition of 209 barley cultivars representative of the European two-rowed spring barley germplasm of the past 190 years. Utilizing high-density SNP marker data, we identified a distinct centromeric haplotype spanning a ~ 250 Mbp large region on chromosome 5H which likely was first introduced into the European breeding germplasm in the early to mid-twentieth century and has been non-recombining and under strong positive selection over the past 70 years. Almost all cultivars in our panel that were released after 2000 carry this new haplotype, suggesting that this region carries one or several genes conferring highly beneficial traits. Using the global barley collection of the German Federal ex situ gene bank at IPK Gatersleben, we found the new haplotype at high frequencies in six-rowed spring-type landraces from Northern Africa, from which it may have been introduced into modern European barley germplasm via southern European landraces. The presence of a 250 Mbp genomic region characterized by lack of recombination and high levels of fixation in modern barley germplasm has substantial implications for the genetic diversity of the modern barley germplasm and for barley breeding.