Integrating QTL Mapping and Candidate-Region Association to Investigate Kernel Size and Weight in Sweet Corn
- 1CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
- 2College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
Abstract
Sweet corn is widely cultivated for fresh consumption and processing, and kernel size and weight are important yield-related traits. However, the genetic architecture of these traits in sweet corn remains poorly understood. In this study, the SHL01 × SHL03 recombinant inbred line (RIL) population was used to investigate the genetic basis of kernel size and weight-related traits using a high-density SNP-based genetic map. Quantitative trait loci (QTL) mapping was conducted in two environments and using the best linear unbiased estimates (BLUEs), followed by candidate-region association analysis to identify candidate genes. A total of 11 unique QTLs were identified from 12 detection records across the two environments and the BLUE dataset. Among them, seven unique QTLs, corresponding to eight detection records, were located on chromosome 7. Several QTLs were located near previously reported loci for kernel-related traits, suggesting a partially shared genetic basis between sweet corn and field corn. Candidate-region association analysis further characterized the major QTL regions and highlighted five potential candidate genes. Among them, Zm00001d020325 (HAK23), encoding a putative potassium transporter, was supported by functional annotation and available expression information, but its haplotypes were not significantly associated with HKW. In contrast, haplotypes defined by variants in neighboring Zm00001d020323 differed in HKW, with the GG haplotype showing the highest mean value. Because these analyses were conducted in overlapping populations, the haplotype results are exploratory. Together, these findings characterize genomic regions associated with mature-kernel traits in sweet corn and identify candidates for further validation.
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BibTeX
@article{ma2026integrating,
title = {{Integrating QTL Mapping and Candidate-Region Association to Investigate Kernel Size and Weight in Sweet Corn}},
author = {Chongjing Ma and Jinrong Song and Jingtao Qu and Hongjian Zheng and Tao Li and Shujun Li and Diansi Yu and Wei Gu and Hui Wang and Kai Li and Yingjie Zhao and Zhixiong Zhao and Felix San Vicente and Ying Xie and Yuan Guan},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = nov,
doi = {10.3390/ijms27219863},
url = {https://www.mdpi.com/1422-0067/27/21/9863},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrating QTL Mapping and Candidate-Region Association to Investigate Kernel Size and Weight in Sweet Corn
AU - Chongjing Ma
AU - Jinrong Song
AU - Jingtao Qu
AU - Hongjian Zheng
AU - Tao Li
AU - Shujun Li
AU - Diansi Yu
AU - Wei Gu
AU - Hui Wang
AU - Kai Li
AU - Yingjie Zhao
AU - Zhixiong Zhao
AU - Felix San Vicente
AU - Ying Xie
AU - Yuan Guan
PY - 2026
DA - 2026/11/03
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219863
UR - https://www.mdpi.com/1422-0067/27/21/9863
AB - Sweet corn is widely cultivated for fresh consumption and processing, and kernel size and weight are important yield-related traits. However, the genetic architecture of these traits in sweet corn remains poorly understood. In this study, the SHL01 × SHL03 recombinant inbred line (RIL) population was used to investigate the genetic basis of kernel size and weight-related traits using a high-density SNP-based genetic map. Quantitative trait loci (QTL) mapping was conducted in two environments and using the best linear unbiased estimates (BLUEs), followed by candidate-region association analysis to identify candidate genes. A total of 11 unique QTLs were identified from 12 detection records across the two environments and the BLUE dataset. Among them, seven unique QTLs, corresponding to eight detection records, were located on chromosome 7. Several QTLs were located near previously reported loci for kernel-related traits, suggesting a partially shared genetic basis between sweet corn and field corn. Candidate-region association analysis further characterized the major QTL regions and highlighted five potential candidate genes. Among them, Zm00001d020325 (HAK23), encoding a putative potassium transporter, was supported by functional annotation and available expression information, but its haplotypes were not significantly associated with HKW. In contrast, haplotypes defined by variants in neighboring Zm00001d020323 differed in HKW, with the GG haplotype showing the highest mean value. Because these analyses were conducted in overlapping populations, the haplotype results are exploratory. Together, these findings characterize genomic regions associated with mature-kernel traits in sweet corn and identify candidates for further validation.
SN - 1422-0067
ER -