A genome-wide analysis of the USDA Soybean Isoline Collection

Erin Gilbert, Ryan Merry, Benjamin W. Campbell, Robert M. Stupar, Aaron J. Lorenz

Research output: Contribution to journalArticlepeer-review


The USDA Soybean Isoline Collection has been an invaluable resource for the soybean genetics and breeding community. This collection, established in 1972, consists of 611 near-isogenic lines (NILs) carrying one or multiple genes conferring traits that had been determined to exhibit Mendelian inheritance. It has been used in multiple studies on the genetic basis, physiology, and agronomy of these qualitative traits. Here, we used publicly available genotype (SoySNP50K), phenotype, and pedigree data on this collection to characterize the isogenicity of the NILs and identify chromosomal positions of unmapped genes. A total of 368 NILs had at least 80% identity to their recurrent parent and, thus, were useful for what can be called introgression mapping. Both on-target and off-target introgressions were evaluated. The size of on-target introgressions into individual NILs ranged from 61 kb to 8.4 Mb, whereas off-target introgressions ranged from 2.6 kb to 54.8 Mb. The observed large off-target introgressions indicated that some NILs carry introgressions nearly the size of an entire chromosome. By applying introgression mapping to genes that had never been mapped, we identified the likely chromosomal positions of six such genes: ab, im, lo, Np, pc, and Rpm. The size of mapping intervals was large in some cases (10.28 Mb for im) but small in others (0.21 Mb for Np). The results reported herein will provide future researchers with a resource to help select informative NILs for future studies, and provide a starting point to further fine map, and ultimately clone and functionally characterize these six soybean genes.

Original languageEnglish (US)
Article numbere20310
JournalPlant Genome
Issue number2
StatePublished - Jun 2023

Bibliographical note

Funding Information:
This work was supported by the Minnesota Soybean Research and Promotion Council and the Minnesota Agricultural Experiment Station. The authors are indebted to Dr. James Specht who provided many great insights into the collection and traits that were analyzed. The manuscript was much improved through his valuable input on an earlier draft. The authors are also appreciative of Dr. Randy Nelson who provided an electronic file containing data on the NILs. Finally, this work and many studies on genetics of soybean would not be possible without the many efforts of Dr. Richard Bernard in creating this collection over a span of several decades.

Publisher Copyright:
© 2023 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't


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