1. Introduction
2. Materials and methods
2.1.Plant materials and phenotypic data collection
2.2.DNA isolation and genome sequencing
2.3.Sequence quality checking,filtering,and align-ment
2.4.Variant calling,filtering,imputation,and anno-tation
2.5.Development of an automated pipeline for vari-ant calling and annotation
2.6.Linkage disequilibrium evaluation
2.7.Population structure evaluation
2.8.Principal component,kinship,and genetic di-versity analyses
2.9.Haplotype construction
2.10.Diversity estimation and selective signature analysis
2.11.Association analysis
3. Results
3.1.Genomic sequence,genotype,linkage disequi-librium,and haplotype
3.2.Genetic diversity and population structure
3.3.Selective signatures and associated genes
3.4.Significant associations in the selective re-gions
3.5.Artificial selection for breeding targets caused the scarcity of high-REC lines
4. Discussion
4.1.Development of a pipeline to construct a varia-tion map of the association panel
4.2.Inbred lines with lower-RECs maintain higher genetic diversity
4.3.Combined use of selective signature and asso-ciation analyses in genetic studies
4.4.Potential synergistic selection of REC and leaf size during modern maize breeding
5.Conclusion
Declaration of competing interest

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maizeEnglish Full Text

Peng Liu;Langlang Ma;Siyi Jian;Yao He;Guangsheng Yuan;Fei Ge;Zhong Chen;Chaoying Zou;Guangtang Pan;Thomas Lübberstedt;Yaou Shen;Xueyong Zhang;Ning Wang;State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/Maize Research Institute, Sichuan Agricultural University;Department of Agronomy, Iowa State University;

Abstract: Genetic transformation has been an effective technology for improving the agronomic traits of maize. However, it is highly reliant on the use of embryonic callus（EC） and shows a serious genotype dependence. In this study, we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline（MQ2Gpipe）. Based on the induction rate of EC（REC）, these inbred lines were categorized into three subpopulations. The low-REC ger... More

Keywords：

maize; genetic transformation; embryonic callus; selective signal; association analysis;

Series：
(D) Agriculture
Subject：
Crop
Classification Code：
S513

Mobile Reading

Read on your phone instantly

Step 1
Scan QR Codes

"Mobile CNKI-CNKI Express" App

Step 2
Open“CNKI Express”

and click the scan icon in the upper left corner of the homepage.

Step 3
Scan QR Codes

Read this article on your phone.
Download
- PDF
- CAJ
Online Reading
- HTML Reading
- Original Reading
AI Summary

Download the mobile appuse the app to scan this coderead the article.

Tips: Please download CAJViewer to view CAJ format full text.

Download: 13 Page: 2178-2195 Pagecount: 18 Size: 4639K

Citation Network

Related Literature

Similar Article
Reader Recommendation
Associated Author

[1]Genome-wide association study of callus induction variation to explore the callus formation mechanism of rice[J]. Zhaoyang Zhang,Hu Zhao,Wei Li,Jiemin Wu,Zaihui Zhou,Fei Zhou,Hao Chen,Yongjun Lin. Journal of Integrative Plant Biology. 2019(11)
[2]Effects of sodium nitroprusside on callus browning of Ficus religiosa: an important medicinal plant[J]. Mohsen Hesami,Masoud Tohidfar,Milad Alizadeh,Mohammad Hosein Daneshvar. Journal of Forestry Research. 2020(03)
[3]Anticancer Activities of Plant Secondary Metabolites: Rice Callus Suspension Culture as a New Paradigm[J]. Wusirika RAMAKRISHNA,Anuradha KUMARI,Nafeesa RAHMAN,Pallavi MandAVE. Rice Science. 2021(01)
[4]Validating field regeneration capacity for selected accessions of Gossypium hirsutum using callus induction and regeneration capacity[J]. TAJO Sani Muhammad,PAN Zhaoe,HE Shoupu,JIA Yinhua,MAHMOOD Tahir,NAZIR Mian Fasil,HU Daowu,WANG Liru,SADAU Salisu Bello,IBRAHIM Sani,AUTA Umar,GENG Xiaoli,DU Xiongming. Journal of Cotton Research. 2023(02)
[5]Validating field regeneration capacity for selected accessions of Gossypium hirsutum using callus induction and regeneration capacity[J]. TAJO Sani Muhammad,PAN Zhaoe,HE Shoupu,JIA Yinhua,MAHMOOD Tahir,NAZIR Mian Fasil,HU Daowu,WANG Liru,SADAU Salisu Bello,IBRAHIM Sani,AUTA Umar,GENG Xiaoli,DU Xiongming. Journal of Cotton Research. 2024(04)
[6]The role of genomic structural variation in the genetic improvement of polyploid crops[J]. Sarah-Veronica Schiessl,Elvis Katche,Elizabeth Ihien,Harmeet Singh Chawla,Annaliese S.Mason. The Crop Journal. 2019(02)
[7]TEAseq-based identification of 35,696 Dissociation insertional mutations facilitates functional genomic studies in maize[J]. Mingjie Lyu,Huafeng Liu,Joram Kiriga Waititu,Ying Sun,Huan Wang,Junjie Fu,Yanhui Chen,Jun Liu,Lixia Ku,Xiliu Cheng. Journal of Genetics and Genomics. 2021(11)
[8]Molecular Marker Development in Post-genomic Era:Leveraging Multiple Resources for Marker Development in Cotton and Other Crops[J]. KUMPATLA Siva P,SHAH Manali R,MUKHOPADHYAY Snehasis,THOMPSON Steven A,GREENE Thomas W. 棉花学报. 2008(S1)
[9]Cytogenetic comparisons between A and G genomes in Oryza using genomic in situ hybridization[J]. Zhi Yong Xiong~(1,2) Guang Xuan Tan~1 Guang Yuan He~2 Guang Cun He~1 Yun Chun Song~11 Key Laboratoty of the Ministry of Education for Plant Developmental Biology,College of Life Sciences,Wuhan University,Wuhan 430072,China.2 China-UK HUST-R Res Genetic Engineering and Genomics Joint Laboratory,Huazhong University of Science and Technology,Wuhan 430074,China. Cell Research. 2006(03)
[10]Effects of plant growth regulators, carbon sources and pH values on callus induction in Aquilaria malaccensis leaf explants and characteristics of the resultant calli[J]. Shashita JAYARAMAN,Nurul Hazwani DAUD,Rasmina HALIS,Rozi MOHAMED. Journal of Forestry Research. 2014(03)

Contents

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maizeEnglish Full Text

Read on your phone instantly

Citation Network

Related Literature