Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size
Grain size is a crucial agronomic trait that significantly impacts yield potential in sorghum (<i>Sorghum bicolor</i>), making it a key focus for genetic improvement. In this study, we investigated the genetic basis of grain size variation using two contrasting sorghum accessions, PI3022...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-06-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/14/12/1791 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849425452604588032 |
|---|---|
| author | Qi Shen Kai Wang Lu Hu Lei Li Lihua Wang Yongfei Wang Yi-Hong Wang Jieqin Li |
| author_facet | Qi Shen Kai Wang Lu Hu Lei Li Lihua Wang Yongfei Wang Yi-Hong Wang Jieqin Li |
| author_sort | Qi Shen |
| collection | DOAJ |
| description | Grain size is a crucial agronomic trait that significantly impacts yield potential in sorghum (<i>Sorghum bicolor</i>), making it a key focus for genetic improvement. In this study, we investigated the genetic basis of grain size variation using two contrasting sorghum accessions, PI302232 (small grain, Sg) and PI563512 (large grain, Lg). The 1000-grain weight, grain length, and grain width of Lg were 3.63-fold, 1.22-fold, and 1.65-fold higher than Sg, respectively. The 1000-grain weight in the F<sub>2</sub> segregating population derived from the cross Sg and Lg parents exhibited the highest phenotypic variation and followed a normal distribution in the three traits. Using bulked segregant analysis sequencing (BSA-seq) with small- and large-grain bulks from the F<sub>2</sub> population, two major quantitative trait loci (QTLs) for grain size were identified on chromosomes 1 and 3. Fine mapping with SSR markers narrowed the <i>qGS1</i> locus to a 1.03 Mb region on chromosome 1 (Chr01: 22,001,448–23,035,593), containing 49 candidate genes. To narrow down potential candidate genes, transcriptome analysis of spike tissues from Sg and Lg at 0 and 14 days after heading revealed 3719 differentially expressed genes (DEGs), primarily enriched in “starch and sucrose metabolism” and “phenylpropanoid biosynthesis” pathways. Integrating fine mapping intervals and RNA-seq data, 6 DEGs were identified within the <i>qGS1</i> region. Quantitative real-time PCR confirmed that 6 genes exhibited different expression at two stages. The expression and bioinformatics analysis showed Sobic.001G230700 was the most likely candidate gene for the qGS1 locus. This study provides new insights into the genetic regulation of grain size and a new target to improve grain size in sorghum. |
| format | Article |
| id | doaj-art-79bbca1cd09a4f218fbc044be88ee100 |
| institution | Kabale University |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj-art-79bbca1cd09a4f218fbc044be88ee1002025-08-20T03:29:45ZengMDPI AGPlants2223-77472025-06-011412179110.3390/plants14121791Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain SizeQi Shen0Kai Wang1Lu Hu2Lei Li3Lihua Wang4Yongfei Wang5Yi-Hong Wang6Jieqin Li7College of Agriculture, Anhui Science and Technology University, Fengyang 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Fengyang 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Fengyang 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Fengyang 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Fengyang 233100, ChinaCollege of Agriculture, Anhui Science and Technology University, Fengyang 233100, ChinaDepartment of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USACollege of Agriculture, Anhui Science and Technology University, Fengyang 233100, ChinaGrain size is a crucial agronomic trait that significantly impacts yield potential in sorghum (<i>Sorghum bicolor</i>), making it a key focus for genetic improvement. In this study, we investigated the genetic basis of grain size variation using two contrasting sorghum accessions, PI302232 (small grain, Sg) and PI563512 (large grain, Lg). The 1000-grain weight, grain length, and grain width of Lg were 3.63-fold, 1.22-fold, and 1.65-fold higher than Sg, respectively. The 1000-grain weight in the F<sub>2</sub> segregating population derived from the cross Sg and Lg parents exhibited the highest phenotypic variation and followed a normal distribution in the three traits. Using bulked segregant analysis sequencing (BSA-seq) with small- and large-grain bulks from the F<sub>2</sub> population, two major quantitative trait loci (QTLs) for grain size were identified on chromosomes 1 and 3. Fine mapping with SSR markers narrowed the <i>qGS1</i> locus to a 1.03 Mb region on chromosome 1 (Chr01: 22,001,448–23,035,593), containing 49 candidate genes. To narrow down potential candidate genes, transcriptome analysis of spike tissues from Sg and Lg at 0 and 14 days after heading revealed 3719 differentially expressed genes (DEGs), primarily enriched in “starch and sucrose metabolism” and “phenylpropanoid biosynthesis” pathways. Integrating fine mapping intervals and RNA-seq data, 6 DEGs were identified within the <i>qGS1</i> region. Quantitative real-time PCR confirmed that 6 genes exhibited different expression at two stages. The expression and bioinformatics analysis showed Sobic.001G230700 was the most likely candidate gene for the qGS1 locus. This study provides new insights into the genetic regulation of grain size and a new target to improve grain size in sorghum.https://www.mdpi.com/2223-7747/14/12/1791sorghumgrain sizeBSA-SeqRNA-Seqcandidate genes |
| spellingShingle | Qi Shen Kai Wang Lu Hu Lei Li Lihua Wang Yongfei Wang Yi-Hong Wang Jieqin Li Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size Plants sorghum grain size BSA-Seq RNA-Seq candidate genes |
| title | Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size |
| title_full | Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size |
| title_fullStr | Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size |
| title_full_unstemmed | Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size |
| title_short | Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for <i>qGS1</i> Related to Sorghum Grain Size |
| title_sort | combined analysis of bsa seq and rna seq reveals candidate genes for i qgs1 i related to sorghum grain size |
| topic | sorghum grain size BSA-Seq RNA-Seq candidate genes |
| url | https://www.mdpi.com/2223-7747/14/12/1791 |
| work_keys_str_mv | AT qishen combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize AT kaiwang combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize AT luhu combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize AT leili combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize AT lihuawang combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize AT yongfeiwang combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize AT yihongwang combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize AT jieqinli combinedanalysisofbsaseqandrnaseqrevealscandidategenesforiqgs1irelatedtosorghumgrainsize |