Knowledge Center Catalog

Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance (Record no. 65778)

MARC details
000 -LEADER
fixed length control field 04256nab|a22005057a|4500
001 - CONTROL NUMBER
control field 65778
003 - CONTROL NUMBER IDENTIFIER
control field MX-TxCIM
005 - DATE AND TIME OF LATEST TRANSACTION
control field 20231019162126.0
008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION
fixed length control field 202210s2022||||mx |||p|op||||00||0|eng|d
022 ## - INTERNATIONAL STANDARD SERIAL NUMBER
International Standard Serial Number 2214-5141
024 8# - OTHER STANDARD IDENTIFIER
Standard number or code https://doi.org/10.1016/j.cj.2022.09.004
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 Yu, G.
9 (RLIN) 13522
245 10 - TITLE STATEMENT
Title Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance
260 ## - PUBLICATION, DISTRIBUTION, ETC. (IMPRINT)
Name of publisher, distributor, etc. Elsevier,
Date of publication, distribution, etc. 2023.
Place of publication, distribution, etc. Netherlands :
500 ## - GENERAL NOTE
General note Peer review
500 ## - GENERAL NOTE
General note Open Access
520 ## - SUMMARY, ETC.
Summary, etc. Genomic selection (GS) is a powerful tool for improving genetic gain in maize breeding. However, its routine application in large-scale breeding pipelines is limited by the high cost of genotyping platforms. Although sequencing-based and array-based genotyping platforms have been used for GS, few studies have compared prediction performance among platforms. In this study, we evaluated the predictabilities of four agronomic traits in 305 maize hybrids derived from 149 parental lines subjected to genotyping by sequencing (GBS), a 40K SNP array, and target sequence capture (TSC) using eight GS models. The GBS marker dataset yielded the highest predictabilities for all traits, followed by TSC and SNP array datasets. We investigated the effect of marker density and statistical models on predictability among genotyping platforms and found that 1K SNPs were sufficient to achieve comparable predictabilities to 10K and all SNPs, and BayesB, GBLUP, and RKHS performed well, while XGBoost performed poorly in most cases. We also selected significant SNP subsets using genome-wide association study (GWAS) analyses in three panels to predict hybrid performance. GWAS facilitated selecting effective SNP subsets for GS and thus reduced genotyping cost, but depended heavily on the GWAS panel. We conclude that there is still room for optimization of the existing SNP array, and using genotyping by target sequencing (GBTS) techniques to integrate a few functional markers identified by GWAS into the 1K SNP array holds great promise of being an effective strategy for developing desirable GS breeding arrays.
546 ## - LANGUAGE NOTE
Language note Text in English
591 ## - CATALOGING NOTES
Affiliation Rodriguez-Chanona, E. : Not in IRS staff list but CIMMYT Affiliation
591 ## - CATALOGING NOTES
Affiliation Guadarrama, A. : Not in IRS staff list but CIMMYT Affiliation
591 ## - CATALOGING NOTES
Affiliation Kehel, Z. : Not in IRS staff list but CIMMYT Affiliation
591 ## - CATALOGING NOTES
Affiliation Chepetla, D. : Not in IRS staff list but CIMMYT Affiliation
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 Maize
Source of heading or term AGROVOC
9 (RLIN) 1173
650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Single nucleotide polymorphisms
Miscellaneous information AGROVOC
9 (RLIN) 10805
650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM
Topical term or geographic name as entry element Hybrids
Source of heading or term AGROVOC
9 (RLIN) 1151
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Cui, Y.
9 (RLIN) 29401
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Jiao, Y.
9 (RLIN) 29402
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Zhou, K.
9 (RLIN) 29403
700 0# - ADDED ENTRY--PERSONAL NAME
Personal name Xin Wang
9 (RLIN) 6995
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Yang, W.
9 (RLIN) 29404
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Xu, Y.
9 (RLIN) 29405
700 1# - ADDED ENTRY--PERSONAL NAME
Personal name Yang, K.
9 (RLIN) 29406
700 0# - ADDED ENTRY--PERSONAL NAME
Personal name Xuecai Zhang
Miscellaneous information Global Maize Program
Field link and sequence number INT3400
9 (RLIN) 951
700 0# - ADDED ENTRY--PERSONAL NAME
Personal name Pengcheng Li
9 (RLIN) 17447
700 0# - ADDED ENTRY--PERSONAL NAME
Personal name Zefeng Yang
9 (RLIN) 17448
700 0# - ADDED ENTRY--PERSONAL NAME
Personal name Yang Xu
9 (RLIN) 17252
700 0# - ADDED ENTRY--PERSONAL NAME
Personal name Chenwu Xu
9 (RLIN) 17254
773 0# - HOST ITEM ENTRY
Title Crop Journal
Related parts v. 11, no. 2, p. 490-498
Place, publisher, and date of publication Netherlands : Elsevier, 2023.
International Standard Serial Number 2214-5141
Record control number 56924
856 ## - ELECTRONIC LOCATION AND ACCESS
Link text Open Access through DSpace
Uniform Resource Identifier https://hdl.handle.net/10883/22283
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
12/07/2022   12/07/2022 Article Not Lost Dewey Decimal Classification     CIMMYT Staff Publications Collection   CIMMYT Knowledge Center: John Woolston Library CIMMYT Knowledge Center: John Woolston Library 12/07/2022

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