Knowledge Center Catalog

Wheat breeding with skim-sequencing for genomic selection: a comparison of marker platforms (Record no. 69557)

MARC details
000 -LEADER
fixed length control field 03398nab|a22003857a|4500
001 - CONTROL NUMBER
control field 69557
003 - CONTROL NUMBER IDENTIFIER
control field MX-TxCIM
005 - DATE AND TIME OF LATEST TRANSACTION
control field 20251124101717.0
008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION
fixed length control field 2511202025|||||xxu||p|op||||00||0|eng|dd
024 8# - OTHER STANDARD IDENTIFIER
Standard number or code http://.doi.org/10.22541/essoar.175096298.87051063/v1
040 ## - CATALOGING SOURCE
Original cataloging agency MX-TxCIM
041 ## - LANGUAGE CODE
Language code of text/sound track or separate title eng
100 1# - MAIN ENTRY--PERSONAL NAME
Personal name Crain, J.L.
9 (RLIN) 4131
245 10 - TITLE STATEMENT
Title Wheat breeding with skim-sequencing for genomic selection: a comparison of marker platforms
260 ## - PUBLICATION, DISTRIBUTION, ETC. (IMPRINT)
Place of publication, distribution, etc. United States of America :
Name of publisher, distributor, etc. Wiley,
Date of publication, distribution, etc. 2025.
500 ## - GENERAL NOTE
General note Preprint
500 ## - GENERAL NOTE
General note Open Access
520 ## - SUMMARY, ETC.
Summary, etc. The promise of predictive genomics-assisted breeding relies on efficient, affordable, and abundant molecular markers. The quantity and quality of markers have greatly expanded, yet plant breeding programs have struggled to fully harness this power mainly using array-based genotyping, targeted amplicon sequencing platforms, or reduced representation, sequence-based genotyping including genotyping-by-sequencing (GBS). Leveraging modern sequencing technology, commercial laboratory products, and open-source software, we demonstrate how ultra-low coverage (skim-seq, 0.05-0.10x) can be a viable marker platform. We genotyped 1,709 wheat lines with GBS, a mid-density DArTAG SNP panel (TaDArTAG vs. 2.0), and skim-seq (0.07x). All skim-seq variants were identified from the pooled skim-seq data and a reference genome without the aid of high-coverage samples. STITCH software was used for imputation followed by filtering to obtain 125,682 markers. Comparing STITCH imputed values to high coverage samples resulted in the correct imputation for more than 96% of the markers. Using phenotypic data, a 5-fold cross validation was implemented for each marker platform. No one marker system performed the best in all test cases, with GBS often resulting in the highest correlation between observed and predicted values. The skim-seq correlations were typically within 0.03 of GBS, suggesting skim-seq can be a viable marker strategy for genomic prediction. As technology and computational pipelines advances, skim-seq appears to be a promising method to bridge the gap between targeted genotyping and whole-genome sequencing. The skim-seq method is highly flexible and can be optimized to a variety of program needs, potentially allowing for wide adoption by the plant breeding community.
546 ## - LANGUAGE NOTE
Language note Text in English
591 ## - CATALOGING NOTES
Affiliation Poland, J.A. : Not in IRS staff list but CIMMYT Affiliation
597 ## - CGIAR Initiative
Donor or Funder United States Agency for International Development (USAID)
-- Foundation for Food & Agriculture Research (FFAR)
-- The Land Institute
-- Malone Family Land Preservation Foundation
650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Marker-assisted selection
Source of heading or term AGROVOC
9 (RLIN) 10737
650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Plant breeding
Source of heading or term AGROVOC
9 (RLIN) 1203
650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Wheat
Source of heading or term AGROVOC
9 (RLIN) 1310
650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Genotyping-by-sequencing
Source of heading or term AGROVOC
9 (RLIN) 1135
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Crossa, J.
Miscellaneous information Genetic Resources Program
Field link and sequence number CCJL01
9 (RLIN) 59
700 0# - ADDED ENTRY--PERSONAL NAME
Personal name Lee DeHaan
9 (RLIN) 40576
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Dreisigacker, S.
Miscellaneous information Global Wheat Program
Field link and sequence number INT2692
9 (RLIN) 851
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Poland, J.A.
9 (RLIN) 2092
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Singh, R.P.
Miscellaneous information Formerly Global Wheat Program
Field link and sequence number INT0610
9 (RLIN) 825
700 1# - ADDED ENTRY--PERSONAL NAME
Field link and sequence number 001713327
Personal name Vitale, P.
Miscellaneous information Genetic Resources Program
9 (RLIN) 31497
773 0# - HOST ITEM ENTRY
Title ESS Open Archive
Related parts In press
Place, publisher, and date of publication United States of America : Wiley, 2025
856 4# - ELECTRONIC LOCATION AND ACCESS
Link text Open Access through DSpace
Uniform Resource Identifier https://hdl.handle.net/10883/36104
942 ## - ADDED ENTRY ELEMENTS (KOHA)
Koha item type Article
Suppress in OPAC No
Source of classification or shelving scheme Dewey Decimal Classification
Holdings
Date last seen Total Checkouts Price effective from Koha item type Lost status Source of classification or shelving scheme Damaged status Not for loan Collection code Withdrawn status Home library Current library Date acquired
11/20/2025   11/20/2025 Article Not Lost Dewey Decimal Classification     CIMMYT Staff Publications Collection   CIMMYT Knowledge Center: John Woolston Library CIMMYT Knowledge Center: John Woolston Library 11/20/2025

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