Fine mapping of yll prioritizes aberrantly spliced Glyma.10G090700 (GmPAO7) as the strongest candidate in a soybean yellow-leaf lethal mutant
- 1School of Life Sciences, Yantai University, Yantai, China
- 2Institute of Cereal and Oil Crops, The Key Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei 050035 China
- 3Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, No.116, Huayuan Road, Zhengzhou, Henan 450002 People’s Republic of China
Abstract
Chlorophyll-deficient mutants are useful for dissecting chloroplast biology in crops. Here, we characterized a recessive soybean (Glycine max (L.) Merr.) yellow-leaf lethal mutant, yll, that showed markedly reduced chlorophyll content, impaired photosystem II performance, and seedling lethality. Fine mapping delimited yll to a 165-kb interval on chromosome 10. In the Wm82.a6.v1 annotation, this interval contains two genes, of which Glyma.10G090700 (GmPAO7) was prioritized as the strongest candidate on the basis of leaf expression, reduced transcript abundance in yll, and a reproducible intron-retention event. Retention of the 110-bp intron between exons 1 and 2 introduced a premature termination codon and was predicted to shorten the annotated 500-aa PAO1-like protein to 32 aa, eliminating the annotated flavin amine oxidase and NAD(P)-binding domains. Direct sequencing of RT-PCR products detected the normally spliced transcript in wild-type plants and the intron-retained sequence in mutant plants, with overlapping splice forms in heterozygous plants; this qualitative assay does not establish splice-isoform proportions. RNA-seq identified broad expression differences between wild-type and mutant sibling seedlings, including enrichment of photosynthesis-, chloroplast-, and redox-associated categories; because yll seedlings were severely chlorotic and developmentally compromised, these profiles are interpreted as the transcriptomic state associated with the phenotype and may largely reflect downstream responses. Transmission electron microscopy revealed chloroplast ultrastructural abnormalities associated with yll, including poorly developed grana and disorganized thylakoid membranes, but these observations do not functionally validate the candidate gene. Together, the mapping and transcript evidence prioritize Glyma.10G090700 (GmPAO7) as the strongest candidate for yll; Glyma.10G091000 remains in the interval, and functional complementation or an independent allele will be required to establish causality. A PAO–polyamine–ROS connection remains a testable hypothesis because PAO activity, polyamine concentrations, and ROS were not measured.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-10015-9.
Related
- Integrated GWAS and linkage mapping in a multi-parent population prioritizes candidate genes for kernel number per row in maize
- REN-former prioritizes candidate regulators of kidney disease-state transitions through single-cell foundation modeling and human genetics
- Integrated computational analysis prioritizes candidate targets and pathways linking ochratoxin A exposure to hepatocellular carcinoma
- Integrative single-cell and bulk transcriptomics with reverse network pharmacology prioritizes macrophage-associated candidate genes in Lyme arthritis
- Cross-scale genetic, molecular, and cellular triangulation prioritizes ACSL5 as a T3-responsive candidate linking hypothyroidism liability to anemia
BibTeX
@article{chen2026fine,
title = {{Fine mapping of yll prioritizes aberrantly spliced Glyma.10G090700 (GmPAO7) as the strongest candidate in a soybean yellow-leaf lethal mutant}},
author = {Lei Chen and Jinwei Feng and Jie Ning and Xiaolei Shi and Xintong Wu and Xiangtai Che and Zhuo Li and Zijun Yu and Xin Wang and Qingquan Chen and Haotong Sun and Yanhu Guo and Luxue Liu and Ziqi Ma and Haichao Li and Jing Lin and Jing Zhao},
journal = {BMC Plant Biology},
year = {2026},
month = sep,
doi = {10.1186/s12870-026-10015-9},
url = {https://doi.org/10.1186/s12870-026-10015-9},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Fine mapping of yll prioritizes aberrantly spliced Glyma.10G090700 (GmPAO7) as the strongest candidate in a soybean yellow-leaf lethal mutant
AU - Lei Chen
AU - Jinwei Feng
AU - Jie Ning
AU - Xiaolei Shi
AU - Xintong Wu
AU - Xiangtai Che
AU - Zhuo Li
AU - Zijun Yu
AU - Xin Wang
AU - Qingquan Chen
AU - Haotong Sun
AU - Yanhu Guo
AU - Luxue Liu
AU - Ziqi Ma
AU - Haichao Li
AU - Jing Lin
AU - Jing Zhao
PY - 2026
DA - 2026/09/25
JO - BMC Plant Biology
DO - 10.1186/s12870-026-10015-9
UR - https://doi.org/10.1186/s12870-026-10015-9
AB - Chlorophyll-deficient mutants are useful for dissecting chloroplast biology in crops. Here, we characterized a recessive soybean (Glycine max (L.) Merr.) yellow-leaf lethal mutant, yll, that showed markedly reduced chlorophyll content, impaired photosystem II performance, and seedling lethality. Fine mapping delimited yll to a 165-kb interval on chromosome 10. In the Wm82.a6.v1 annotation, this interval contains two genes, of which Glyma.10G090700 (GmPAO7) was prioritized as the strongest candidate on the basis of leaf expression, reduced transcript abundance in yll, and a reproducible intron-retention event. Retention of the 110-bp intron between exons 1 and 2 introduced a premature termination codon and was predicted to shorten the annotated 500-aa PAO1-like protein to 32 aa, eliminating the annotated flavin amine oxidase and NAD(P)-binding domains. Direct sequencing of RT-PCR products detected the normally spliced transcript in wild-type plants and the intron-retained sequence in mutant plants, with overlapping splice forms in heterozygous plants; this qualitative assay does not establish splice-isoform proportions. RNA-seq identified broad expression differences between wild-type and mutant sibling seedlings, including enrichment of photosynthesis-, chloroplast-, and redox-associated categories; because yll seedlings were severely chlorotic and developmentally compromised, these profiles are interpreted as the transcriptomic state associated with the phenotype and may largely reflect downstream responses. Transmission electron microscopy revealed chloroplast ultrastructural abnormalities associated with yll, including poorly developed grana and disorganized thylakoid membranes, but these observations do not functionally validate the candidate gene. Together, the mapping and transcript evidence prioritize Glyma.10G090700 (GmPAO7) as the strongest candidate for yll; Glyma.10G091000 remains in the interval, and functional complementation or an independent allele will be required to establish causality. A PAO–polyamine–ROS connection remains a testable hypothesis because PAO activity, polyamine concentrations, and ROS were not measured. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-10015-9.
SN - 1471-2229
ER -