High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping Qtls of Resistance to Aspergillus Flavus Infection in Peanut

Abstract Cultivated peanut (Arachis hypogaea L.) is rich in edible oil and protein, which is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanut, hindering the development of peanut industry and threatening consumers’ health. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for control the aflatoxin contamination, and understanding of the genetic basis of resistance is vital to its genetic enhancement. In this study, we report the QTL mapping of resistance to A. flavus infection of a well-known resistant variety J11. A recombination inbred line (RIL) population was constructed by crossing a susceptible variety Zhonghua 16 and J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of infection index in four consecutive years, six novel resistant QTLs were identified and they explained 5.03-10.87% phenotypic variances. The favorable alleles of five QTLs were from J11 while that of one QTL were from Zhonghua 16. The pyramiding of these favorable alleles significantly improved the resistance to A. flavus infection. These results could contribute greatly to understanding of genetic basis of A. flavus resistance and could be meaningful in further resistance improvement in peanut.

Download Full-text

High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping QTLs of Resistance to Aspergillus flavus Infection in Peanut

Frontiers in Plant Science ◽

10.3389/fpls.2021.745408 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yifei Jiang ◽

Huaiyong Luo ◽

Bolun Yu ◽

Yingbin Ding ◽

Yanping Kang ◽

...

Keyword(s):

Linkage Map ◽

Aspergillus Flavus ◽

Genetic Linkage ◽

Genetic Basis ◽

Genetic Linkage Map ◽

Aflatoxin Contamination ◽

Whole Genome ◽

Genome Resequencing ◽

Favorable Alleles ◽

Whole Genome Resequencing

The cultivated peanut (Arachis hypogaea L.), which is rich in edible oil and protein, is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanuts, hindering the development of the peanut industry and threatening the health of consumers. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for the control of aflatoxin contamination, and understanding the genetic basis of resistance is vital to its genetic enhancement. In this study, we reported the quantitative trait locus (QTL) mapping of resistance to A. flavus infection of a well-known resistant variety, J11. A mapping population consisting of 200 recombinant inbred lines (RILs) was constructed by crossing a susceptible variety, Zhonghua 16, with J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of an infection index in 4 consecutive years, six novel resistant QTLs with 5.03–10.87% phenotypic variances explained (PVE) were identified on chromosomes A05, A08, B01, B03, and B10. The favorable alleles of five QTLs were from J11, while that of one QTL was from Zhonghua 16. The combination of these favorable alleles significantly improved resistance to A. flavus infection. These results could contribute greatly to the understanding of the genetic basis of A. flavus resistance and could be meaningful in the improvement of further resistance in peanuts.

Download Full-text

Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽

10.3390/horticulturae7120534 ◽

2021 ◽

Vol 7 (12) ◽

pp. 534

Author(s):

Zhijiang Wu ◽

Haiyan Deng ◽

Guidong Liang ◽

Xiaoying Ye ◽

Yonghua Qin ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Snp Markers ◽

High Density ◽

Genetic Maps ◽

Fleshy Fruit ◽

Whole Genome ◽

Genome Resequencing ◽

Hylocereus Undatus ◽

Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

Download Full-text

Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

Molecular Plant ◽

10.1016/j.molp.2018.11.007 ◽

2019 ◽

Vol 12 (1) ◽

pp. 30-43 ◽

Cited By ~ 47

Author(s):

Dezhi Wu ◽

Zhe Liang ◽

Tao Yan ◽

Ying Xu ◽

Lijie Xuan ◽

...

Keyword(s):

Genetic Basis ◽

Whole Genome ◽

Genome Resequencing ◽

Whole Genome Resequencing

Download Full-text

Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data

Breeding Science ◽

10.1270/jsbbs.66.244 ◽

2016 ◽

Vol 66 (2) ◽

pp. 244-259 ◽

Cited By ~ 14

Author(s):

Shi Liu ◽

Peng Gao ◽

Qianglong Zhu ◽

Feishi Luan ◽

Angela R. Davis ◽

...

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Citrullus Lanatus ◽

Whole Genome ◽

Sequencing Data ◽

Cleaved Amplified Polymorphic Sequence

Download Full-text

A genetic linkage map for the ectomycorrhizal fungusLaccaria bicolorand its alignment to the whole-genome sequence assemblies

New Phytologist ◽

10.1111/j.1469-8137.2008.02614.x ◽

2008 ◽

Vol 180 (2) ◽

pp. 316-328 ◽

Cited By ~ 27

Author(s):

J. Labbé ◽

X. Zhang ◽

T. Yin ◽

J. Schmutz ◽

J. Grimwood ◽

...

Keyword(s):

Linkage Map ◽

Genome Sequence ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Whole Genome Sequence ◽

Whole Genome

Download Full-text

Mapping of a major QTL controlling plant height using a high-density genetic map and QTL-seq methods based on whole-genome resequencing in Brassica napus

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab118 ◽

2021 ◽

Author(s):

Zhixue Dong ◽

Muhammad khorshed Alam ◽

Meili Xie ◽

Li Yang ◽

Jie Liu ◽

...

Keyword(s):

Brassica Napus ◽

Linkage Map ◽

Plant Height ◽

Interval Mapping ◽

High Density ◽

Whole Genome ◽

Genome Resequencing ◽

Whole Genome Resequencing ◽

High Density Linkage Map ◽

Major Qtl

Abstract Plant height is a crucial element related to plant architecture that influences the seed yield of oilseed rape (Brassica napus L.). In this study, we isolated a natural B. napus mutant, namely a semi-dwarf mutant (sdw-e), which exhibits a 30% reduction in plant height compared to Zhongshuang 11-HP (ZS11-HP). Quantitative trait locus sequencing (QTL-seq) was conducted using two extreme DNA bulks in F2 populations in Wuchang-2017 derived from ZS11-HP × sdw-e to identify QTLs associated with plant height. The result suggested that two QTL intervals were located on chromosome A10. The F2 population consisting of 200 individuals in Yangluo-2018 derived from ZS11-HP × sdw-e was used to construct a high-density linkage map using whole-genome resequencing. The high-density linkage map harbored 4323 bin markers and covered a total distance of 2026.52 cM with an average marker interval of 0.47 cM. The major QTL for plant height named qPHA10 was identified on linkage group A10 by interval mapping (IM) and composite interval mapping (CIM) methods. The major QTL qPHA10 was highly consistent with the QTL-seq results. And then, we integrated the variation sites and expression levels of genes in the major QTL interval to predict the candidate genes. Thus, the identified QTL and candidate genes could be used in marker-assisted selection for B. napus breeding in the future.

Download Full-text