Abstract
Peanut (Arachis hypogaea L.) is globally recognized as an important oilseed crop. Traits related to plant architecture are closely associated with yield in peanut. In this study, we focused on four specific traits related to plant architecture-first branch length (FBL), main stem height (MSH), stem diameter (SD), and the number of nodes on the main stem (NSK)-across three locations. Using whole-genome resequencing data from a genetically diverse collection of peanut landraces, we conducted a genome-wide association study analysis to identify genetic variants associated with these traits. Notably, a novel genomic region on Arahy.03:39916768-42652757 was associated with SD for the first time. Homology analysis suggested that two annotated genes within this region may contribute to stem elongation and seed development. For MSH, NSK, and FBL, more than half of the significantly associated single-nucleotide polymorphisms (SNPs) were localized on chromosome Arahy.05. Two SNPs at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for MSH and FBL: one homologous gene near these SNPs encoded an E3 ubiquitin-protein ligase, while the other encodes cinnamyl alcohol dehydrogenase. Additionally, one SNP at Arahy.05:53493734 was identified as a potential diagnostic marker for MSH, FBL, and NSK and validated using the penta-primer amplification refractory mutation system and quantitative real-time polymerase chain reaction. A gene near this SNP belongs to the protein kinase superfamily. Enzymes are known to regulate diverse cellular and biological processes, including plant development. These findings advance our understanding of the genetic basis of peanut architecture and provide valuable markers for future yield improvement efforts.
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Claims 9
Claim · model-written summary
A novel Arahy.03 region was associated with stem diameter.
- Taxon
- Peanut
Arachis hypogaeat0 - Gene
- Arahy.03:39916768-42652757e0
- Outcome
- SDe0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a novel genomic region on Arahy.03:39916768-42652757 was associated with SD for the first time”
t0“peanut”
Claim · model-written summary
Two annotated genes in the region may contribute to stem elongation and seed development.
- Taxon
- PeanutArachis hypogaeat0
- Gene
- two annotated genese0
- Outcome
- stem elongation and seed developmente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“two annotated genes within this region may contribute to stem elongation and seed development”
t0“peanut”
Claim · model-written summary
More than half of significant SNPs for main-stem height, node number and first-branch length localized to Arahy.05.
- Taxon
- PeanutArachis hypogaeat0
- Outcome
- single-nucleotide polymorphisms (SNPs) were localized on chromosome Arahy.05e0
- Value
- more than halfe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“For MSH, NSK, and FBL, more than half of the significantly associated single-nucleotide polymorphisms (SNPs) were localized on chromosome Arahy.05”
t0“peanut”
Claim · model-written summary
Arahy.09:112028951 was a potential diagnostic SNP for main-stem height and first-branch length.
- Taxon
- PeanutArachis hypogaeat0
- Gene
- Arahy.09:112028951e0
- Outcome
- potential diagnostic markers for MSH and FBLe0
- Value
- Two SNPse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Two SNPs at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for MSH and FBL”
t0“peanut”
Claim · model-written summary
Arahy.09:112272948 was a potential diagnostic SNP for main-stem height and first-branch length.
- Taxon
- PeanutArachis hypogaeat0
- Gene
- Arahy.09:112272948e0
- Outcome
- potential diagnostic markers for MSH and FBLe0
- Value
- Two SNPse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Two SNPs at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for MSH and FBL”
t0“peanut”
Claim · model-written summary
A gene near these SNPs encoded an E3 ubiquitin-protein ligase.
- Taxon
- PeanutArachis hypogaeat0
- Gene
- one homologous genee0
- Outcome
- encoded an E3 ubiquitin-protein ligasee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“one homologous gene near these SNPs encoded an E3 ubiquitin-protein ligase”
t0“peanut”
Claim · model-written summary
Another nearby gene encoded cinnamyl alcohol dehydrogenase.
- Taxon
- PeanutArachis hypogaeat0
- Gene
- cinnamyl alcohol dehydrogenasee0
- Outcome
- encodes cinnamyl alcohol dehydrogenasee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the other encodes cinnamyl alcohol dehydrogenase”
t0“peanut”
Claim · model-written summary
Arahy.05:53493734 was a potential diagnostic marker for three architecture traits and was validated.
- Taxon
- PeanutArachis hypogaeat0
- Gene
- Arahy.05:53493734e0
- Outcome
- potential diagnostic marker for MSH, FBL, and NSKe0
- Value
- one SNPe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“one SNP at Arahy.05:53493734 was identified as a potential diagnostic marker for MSH, FBL, and NSK and validated using the penta-primer amplification refractory mutation system and quantitative real-time polymerase chain reaction”
t0“peanut”
Claim · model-written summary
A gene near Arahy.05:53493734 belongs to the protein kinase superfamily.
- Taxon
- PeanutArachis hypogaeat0
- Gene
- A genee0
- Outcome
- belongs to the protein kinase superfamilye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A gene near this SNP belongs to the protein kinase superfamily”
t0“peanut”