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130
result(s) for
"Xu, Linhong"
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Candidate gene identification and marker development for seed coat peeling rate in peanut (Arachis Hypogaea L.)
2025
Background
Cultivated peanut (
Arachis hypogaea
L.) is an important economic and oilseed crop in China. The seed coat plays a crucial role in resisting pests and diseases, and seed coat peeling rate (SCPR) is a key factor influencing the efficiency and quality of mechanical shelling. Given the high kernel breakage rate and susceptibility to
Aspergillus flavus
infection during mechanical shelling, gene mining for SCPR holds significant theoretical and practical value. However, the genetic basis of SCPR has rarely been reported.
Results
This study represented the first identification of genetic loci associated with SCPR in peanut. A genome-wide association study (GWAS) was conducted on a natural population comprising 353 peanut accessions, while quantitative trait locus (QTL) mapping was performed using a recombinant inbred line (RIL) population of 521 lines derived from YZ9102 and WT09-0023. GWAS analysis revealed a significantly associated genomic region at the distal end of chromosome 5, encompassing 111 significant single nucleotide polymorphisms (SNPs), among which six SNPs were consistently detected across two environments and exhibited strong linkage with SCPR. QTL mapping identified five QTLs associated with SCPR, located on chromosomes A04, A05, A09, A10, and A18, with LOD scores ranging from 3.06 to 5.54. Notably, the co-localization of GWAS signals and QTL mapping at the distal end of chromosome 5 suggests that
qSCPRA05
represents a stable and major QTL governing SCPR in peanut, spanning a 385.66 kb physical interval (
Arahy.05:114
,
895
,
772 − 115
,
281
,
432
). Within this region, three linkage disequilibrium (LD) blocks were detected, harboring 33 candidate genes. Among them,
Arahy.0C6ZNN
, which encodes laccase, was identified as the most likely candidate gene through integration of sequence variation analysis between the RIL parental lines and functional gene annotation. Furthermore, a functional marker
A05.114993389
was developed and validated in both the natural and RIL populations, providing a valuable genomic resource for marker-assisted selection (MAS) in peanut breeding programs.
Conclusions
This study represented the gene mining of SCPR in peanut, providing novel insights into its genetic basis and laying a foundation for elucidating the underlying regulatory mechanisms. The identification of a major QTL
qSCPRA05
and the candidate gene
Arahy.0C6ZNN
may offer valuable targets for further functional research. Moreover, the development of molecular markers linked to SCPR presents a promising tool for marker-assisted selection (MAS), facilitating genetic improvement and accelerating breeding efforts for enhanced seed coat integrity in peanut.
Journal Article
Research on the Micro-Extrusion Process of Copper T2 with Different Ultrasonic Vibration Modes
2019
As an effective method for the fabrication of miniature metallic parts, the development of micro-forming process (MFP) is still restricted by the existence of size effect. To improve the micro-forming performance of metal material, ultrasonic vibration assisted MFP had been studied extensively for its superiorities in improving materials flow stress and reducing interfacial friction. However, from the literature available, the high frequency vibration was usually found to be superimposed on the forming tool while seldom on the workpiece. Our group developed a special porous sonotrode platform which can realize tool vibration and workpiece ultrasonic vibration independently. In this work, ultrasonic micro-extrusion experiments for copper T2 material under tool vibration and the workpiece vibration condition, respectively, were conducted for comparing the micro-forming characteristic of different vibration modes. The micro-extrusion experiment results of copper T2 show that the lower extrusion flow stress, the higher micro-extrusion formability and surface micro-hardness, and more obvious grain refinement phenomenon can be obtained under the workpiece vibration condition compared with that of tool vibration. These findings may enhance our understanding on different ultrasonic forming mechanisms and energy transmission efficiency under two different vibration modes.
Journal Article
The complete chloroplast genome sequence of Santalum album
2020
The first complete chloroplast genome (cpDNA) sequence of Santalum album was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 144,101 bp in length, contains a large single copy region (LSC) of 83,796 bp and a small single copy region (SSC) of 11,277 bp, which were separated by a pair of inverted repeats (IR) regions of 24,514 bp. The genome contains 123 genes, including 80 protein-coding genes, 8 ribosomal RNA genes, and 35 transfer RNA genes. The overall GC content of the whole genome is 38.0%, and the corresponding values of the LSC, SSC, and IR regions are 35.9%, 31.4%, and 43.1%, respectively. Further phylogenomic analysis showed that S. album and Osyris alba clustered in a clade in Santalales order.
Journal Article
The complete chloroplast genome sequence of Garcinia pedunculata
2020
The first complete chloroplast genome (cpDNA) sequence of Garcinia pedunculata was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 157,688 bp in length, contains a large single copy region (LSC) of 85,994 bp and a small single copy region (SSC) of 17,656 bp, which were separated by a pair of inverted repeats (IR) regions of 27,017 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.2%, and the corresponding values of the LSC, SSC, and IR regions are 33.6%, 30.2%, and 42.2%, respectively. Further phylogenomic analysis showed that G. pedunculata and Garcinia mangostana clustered in a clade in order Malpighiales.
Journal Article
The complete chloroplast genome sequence of Altingia yunnanensis
2020
The first complete chloroplast genome (cpDNA) sequence of Altingia yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,860 bp in length, contains a large single-copy region (LSC) of 89,162 bp and a small single-copy region (SSC) of 19,008 bp, which were separated by a pair of inverted repeat (IR) regions of 26,325 bp each. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further, the phylogenomic analysis showed that A. yunnanensis and Altingia excelsa clustered in a clade in Saxifragales order.
Journal Article
The complete chloroplast genome sequence of Litsea garrettii
2020
The first complete chloroplast genome (cpDNA) sequence of Litsea garrettii was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 154,011 bp in length, contains a large single-copy region (LSC) of 93,697 bp and a small single-copy region (SSC) of 18,826 bp, which were separated by a pair of inverted repeat (IR) regions of 20,744 bp. The genome contains 127 genes, including 82 protein-coding genes, 8 ribosomal RNA genes, and 36 transfer RNA genes. Further phylogenomic analysis showed that L. garrettii and Parasassafras confertiflorum clustered in a clade in Lauraceae family.
Journal Article
The complete chloroplast genome sequence of Casimiroa edulis
2019
The first complete chloroplast genome (cpDNA) sequence of Casimiroa edulis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,176 bp in length, contains a large single-copy region (LSC) of 87,536 bp and a small single-copy region (SSC) of 18,576 bp, which were separated by a pair of inverted repeats (IR) regions of 27,032 bp. The genome contains 131 genes, including 86 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 38.2%, and the corresponding values of the LSC, SSC, and IR regions are 36.5, 33.0, and 42.9%, respectively. Further, phylogenomic analysis showed that C. edulis, Phellodendron amurense, and Zanthoxylum bungeanum clustered in a clade in family Rutaceae.
Journal Article
The complete chloroplast genome sequence of Altingia excelsa
2020
The first complete chloroplast genome (cpDNA) sequence of Altingia excelsa was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,861 bp in length, contains a large single copy region (LSC) of 89,126 bp and a small single copy region (SSC) of 19,011 bp, which were separated by a pair of inverted repeats (IR) regions of 26,362 bp each. The genome contains 127 genes, including 82 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenomic analysis showed that A. excelsa and Liquidambar formosana clustered in a clade in Saxifragales order.
Journal Article
The complete chloroplast genome of Pouteria caimito
2019
The first complete chloroplast genome sequences of Pouteria caimito were reported in this study. The cpDNA of P. caimito is 158,937 bp in length, contains a large single-copy region (LSC) of 88,100 bp and a small single-copy region (SSC) of 18,631 bp, which were separated by a pair of inverted repeat (IR) regions of 26,103 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.8%. Phylogenetic analysis of 15 chloroplast genomes within the order Ericales suggests that P. caimito is closely related to Pouteria campechiana.
Journal Article
The complete chloroplast genome of Streblus indicus
2019
The first complete chloroplast genome sequences of Streblus indicus were reported in this study. The cpDNA of S. indicus is 159,853 bp in length, contains a large single copy region (LSC) of 88,950 bp and a small single copy region (SSC) of 19,313 bp, which were separated by a pair of inverted repeat (IR) regions of 25,795 bp. The genome contains 129 genes, including 84 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.1%. Phylogenetic analysis of 14 chloroplast genomes within the family Moraceae shows that S. indicus clustered in a unique clade.
Journal Article