Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences

Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explore the distribution of recombination and potential chromosomal rearrangements. This linkage map was then used to identify Quantitative Trait Loci (QTL) for seed and pod traits that were phenotyped over three consecutive years for the purpose of developing trait-associated markers for breeding. Forty-nine QTL were identified in 14 LG for seed size index, kernel percentage, seed weight, pod weight, single-kernel, double-kernel, pod area and pod density. Twenty QTL demonstrated phenotypic variance explained (PVE) greater than 10% and eight more than 20%. Of note, seven of the eight major QTL for pod area, pod weight and seed weight (PVE >20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner.

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Pod and seed trait QTL identification to assist breeding for peanut market preferences

10.1101/738914 ◽

2019 ◽

Cited By ~ 1

Author(s):

Carolina Chavarro ◽

Ye Chu ◽

Corley Holbrook ◽

Thomas Isleib ◽

David Bertioli ◽

...

Keyword(s):

Seed Weight ◽

Chromosomal Rearrangements ◽

Snp Array ◽

Phenotypic Variance ◽

Linkage Groups ◽

Single Linkage ◽

Size Index ◽

Peanut Genome ◽

Qtl Identification ◽

Variance Explained

ABSTRACTAlthough seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explorethe distribution of recombination and potential chromosomal rearrangements. These traits were phenotyped over three consecutive years for the purpose of developing trait-associated markers for breeding. Forty-nine QTL were identified in 14 LG for seed size index, kernel percentage, seed weight, pod weight, single-kernel, double-kernel, pod area and pod density. Twenty QTL demonstrated phenotypic variance explained (PVE) greater than 10% and eight more than 20%. Of note, seven of the eight major QTL for pod area, pod weight and seed weight (PVE >20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner.

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QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.)

BMC Plant Biology ◽

10.1186/s12870-019-2164-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 6

Author(s):

Shengzhong Zhang ◽

Xiaohui Hu ◽

Huarong Miao ◽

Ye Chu ◽

Fenggao Cui ◽

...

Keyword(s):

Genetic Map ◽

Seed Weight ◽

Genome Wide Association Study ◽

Bulked Segregant Analysis ◽

High Density ◽

Width Ratio ◽

Phenotypic Variance ◽

Phenotypic Data ◽

Cultivated Peanut ◽

Peanut Genome

Abstract Background The cultivated peanut is an important oil and cash crop grown worldwide. To meet the growing demand for peanut production each year, genetic studies and enhanced selection efficiency are essential, including linkage mapping, genome-wide association study, bulked-segregant analysis and marker-assisted selection. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for high density genetic map (HDGM) construction and quantitative trait loci (QTLs) mapping. In this study, a HDGM was constructed using SLAF-seq leading to identification of QTL for seed weight and size in peanut. Results A recombinant inbred line (RIL) population was advanced from a cross between a cultivar ‘Huayu36’ and a germplasm line ‘6–13’ with contrasting seed weight, size and shape. Based on the cultivated peanut genome, a HDGM was constructed with 3866 loci consisting of SLAF-seq and simple sequence repeat (SSR) markers distributed on 20 linkage groups (LGs) covering a total map distance of 1266.87 cM. Phenotypic data of four seed related traits were obtained in four environments, which mostly displayed normal distribution with varied levels of correlation. A total of 27 QTLs for 100 seed weight (100SW), seed length (SL), seed width (SW) and length to width ratio (L/W) were identified on 8 chromosomes, with LOD values of 3.16–31.55 and explaining phenotypic variance (PVE) from 0.74 to 83.23%. Two stable QTL regions were identified on chromosomes 2 and 16, and gene content within these regions provided valuable information for further functional analysis of yield component traits. Conclusions This study represents a new HDGM based on the cultivated peanut genome using SLAF-seq and SSRs. QTL mapping of four seed related traits revealed two stable QTL regions on chromosomes 2 and 16, which not only facilitate fine mapping and cloning these genes, but also provide opportunity for molecular breeding of new peanut cultivars with improved seed weight and size.

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A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.041319 ◽

2017 ◽

Vol 7 (7) ◽

pp. 2353-2361 ◽

Cited By ~ 8

Author(s):

Jacob A Tennessen ◽

Stephanie R Bollmann ◽

Michael S Blouin

Keyword(s):

Linkage Map ◽

Chromosomal Rearrangements ◽

Biomphalaria Glabrata ◽

Linkage Groups ◽

Genome Sequences ◽

Human Parasite ◽

Causal Genes ◽

Targeted Capture ◽

Future Work ◽

Linkage Relationships

Abstract The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail–schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite.

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Development and validation of 58K SNP-array and high-density linkage map in Nile tilapia (O. niloticus)

10.1101/322826 ◽

2018 ◽

Cited By ~ 5

Author(s):

Rajesh Joshi ◽

Mariann Árnyasi ◽

Sigbjørn Lien ◽

Hans Magnus Gjøen ◽

Alejandro Tola Alvarez ◽

...

Keyword(s):

Linkage Map ◽

Genome Assembly ◽

Nile Tilapia ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Polymorphic Information Content ◽

Snp Array ◽

High Density ◽

Reference Sequence ◽

Linkage Groups

AbstractDespite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia (Oreochromis niloticus). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 of the SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O_niloticus_UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups. Around one-third of the linkage groups showed a different recombination rate between sexes, with male and female map lengths differing by a factor of 1.2 (1359.6cM and 1632.9cM respectively), with most linkage groups displayed a sigmoid recombination profile. Finally, the sex-determining locus in this population was mapped to position 40.53 cM on linkage group 23, in the vicinity of the anti-Müllerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasive traits in tilapia.

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Secondary Trisomics and Telotrisomics of Rice: Origin, Characterization, and Use in Determining the Orientation of Chromosome Map

Genetics ◽

10.1093/genetics/143.1.517 ◽

1996 ◽

Vol 143 (1) ◽

pp. 517-529

Author(s):

Kuldeep Singh ◽

D S Multani ◽

Gurdev S Khush

Keyword(s):

Linkage Map ◽

Large Population ◽

Marker Genes ◽

Linkage Groups ◽

Breeding Behavior ◽

Specific Chromosome ◽

Chromosome Map ◽

Primary Trisomics ◽

Correct Orientation ◽

Genetic Segregation

Abstract Secondary trisomics and telotrisomics representing the 12 chromosomes of rice were isolated from the progenies of primary trisomics. A large population of each primary trisomic was grown. Plants showing variation in gross morphology compared to the primary trisomics and disomic sibs were selected and analyzed cytologically at diakinesis and pachytene. Secondary trisomics for both arms of chromosomes 1, 2, 6, 7 and 11 and for one arm of chromosomes 4, 5, 8, 9 and 12 were identified. Telotrisomics for short arm of chromosomes 1, 8, 9 and 10 and for long arms of chromosomes 2, 3 and 5 were isolated. These secondary and telotrisomics were characterized morphologically and for breeding behavior. Secondary trisomics 2n + 1S · 1S, 2n + 1L · 1L, 2n + 2S · 2S, 2n + 2L · 2L, 2n + 6S · 6S, 2n + 6L · 6L and 2n + 7L · 7L are highly sterile, and 2n + 1L · 1L, 2n + 2L · 2L and 2n + 7L · 7L do not set any seed even upon backcrossing. Telotrisomics are fertile and vigorous. Genetic segregation of 43 marker genes was studied in the F2 or backcross progenies. On the basis of segregation data, these genes were delimited to specific chromosome arms. Correct orientation of 10 linkage groups was determined and centromere positions on nine linkage groups were approximated. A revised linkage map of rice is presented.

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An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽

10.1139/g01-144 ◽

2002 ◽

Vol 45 (2) ◽

pp. 282-295 ◽

Cited By ~ 175

Author(s):

Elizabeth S Jones ◽

Natalia L Mahoney ◽

Michael D Hayward ◽

Ian P Armstead ◽

J Gilbert Jones ◽

...

Keyword(s):

Molecular Marker ◽

Linkage Map ◽

Genetic Map ◽

Lolium Perenne ◽

Perennial Ryegrass ◽

Genetic Linkage Map ◽

Population Based ◽

Genetic Maps ◽

Linkage Groups ◽

Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

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A genetic linkage map for the domesticated silkworm, Bombyx mori, based on restriction fragment length polymorphisms

Genetics Research ◽

10.1017/s0016672300034467 ◽

1995 ◽

Vol 66 (2) ◽

pp. 109-126 ◽

Cited By ~ 48

Author(s):

Jinrui Shi ◽

David G. Heckel ◽

Marian R. Goldsmith

Keyword(s):

Linkage Map ◽

Bombyx Mori ◽

Restriction Fragment ◽

Fragment Length ◽

Restriction Fragment Length Polymorphisms ◽

Genetic Maps ◽

Crossing Over ◽

Linkage Groups ◽

Length Polymorphisms ◽

Restriction Fragment Length

SummaryWe present data for the initial construction of a molecular linkage map for the domesticated silkworm, Bombyx mori, based on 52 progeny from an F2 cross from a pair mating of inbred strains p50 and C108, using restriction fragment length polymorphisms (RFLPs). The map contains 15 characterized single copy sequences, 36 anonymous sequences derived from a follicular cDNA library, and 10 loci corresponding to a low copy number retrotransposon, mag. The 15 linkage groups and 8 ungrouped loci account for 23 of the 28 chromosomes and span a total recombination length of 413 cM; 10 linkage groups were correlated with established classic genetic maps. Scoring data from Southern blots were analysed using two Pascal programs written specifically to analyse linkage data in Lepidoptera, where females are the heterogametic sex and have achiasmatic meiosis (no crossing-over). These first examine evidence for linkage by calculating the maximum lod score under the hypothesis that the two loci are linked over the likelihood under the hypothesis that the two loci assort independently, and then determine multilocus linkage maps for groups of putatively syntenic loci by calculating the maximum likelihood estimate of the recombination fractions and the log likelihood using the EM algorithm for a specified order of loci along the chromosome. In addition, the possibility of spurious linkage was exhaustively tested by searching for genotypes forbidden by the absence of crossing-over in one sex.

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GxEsum: a novel approach to estimate the phenotypic variance explained by genome-wide GxE interaction based on GWAS summary statistics for biobank-scale data

Genome Biology ◽

10.1186/s13059-021-02403-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jisu Shin ◽

Sang Hong Lee

Keyword(s):

Complex Traits ◽

Error Rates ◽

Type I ◽

Phenotypic Variance ◽

Environment Interaction ◽

Summary Statistics ◽

Gxe Interaction ◽

Genome Wide ◽

Scale Data ◽

Variance Explained

AbstractGenetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. However, existing methods are computationally demanding and infeasible to handle biobank-scale data. Here, we introduce GxEsum, a method for estimating the phenotypic variance explained by genome-wide GxE based on GWAS summary statistics. Through comprehensive simulations and analysis of UK Biobank with 288,837 individuals, we show that GxEsum can handle a large-scale biobank dataset with controlled type I error rates and unbiased GxE estimates, and its computational efficiency can be hundreds of times higher than existing GxE methods.

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Genetic linkage map of Phaseolus vulgaris and identification of QTLs responsible for resistance to Xanthomonas axonopodis pv. phaseoli

Fitopatologia Brasileira ◽

10.1590/s0100-41582003000100001 ◽

2003 ◽

Vol 28 (1) ◽

pp. 5-10 ◽

Cited By ~ 7

Author(s):

Amaury S. Santos ◽

Ricardo E. Bressan-Smith ◽

Messias G. Pereira ◽

Rosana Rodrigues ◽

Claudia F. Ferreira

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Linkage Map ◽

Linkage Groups ◽

Resistant Genotype ◽

Xanthomonas Axonopodis ◽

Low Degree ◽

Phenotypic Variations ◽

Genomic Regions ◽

High Degree

Common bean (Phaseolus vulgaris) cultivars with a high degree of resistance to Xanthomonas axonopodis pv. phaseoli (Xap) are not available in Brazil. Despite many studies, a low degree of resistance to Xap continues to exist due to its complex genetic inheritance, which is not well known. The objectives of this research were to complement a common bean genetic map based on the cross between a susceptible genotype 'HAB-52' and a resistant genotype 'BAC-6', and to map and analyze genomic regions (quantitative trait loci – QTLs) related to Xap resistance. Eleven linkage groups were determined using 143 RAPD markers, covering 1,234.5 cM of the genome. This map was used to detect QTLs associated with Xap resistance on leaves and pods. The averages of disease severity on leaves (represented by the transformed disease index – TDI) and pods (represented by the diameter of lesion on pods – DLP) were added to the data of the linkage map. Five TDI QTLs and only one LDP QTL were detected. The TDI QTLs were placed in the A, B, G and J linkage groups, with phenotypic variations ranging from 12.7 to 71.6%. The DLP QTL explained 12.9% of the phenotypic variation and was mapped in a distinct linkage group. These results indicate that there are different genes involved in the control of resistance on leaves and pods.

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Patterns of genome duplication within the Brassica napus genome

Genome ◽

10.1139/g03-006 ◽

2003 ◽

Vol 46 (2) ◽

pp. 291-303 ◽

Cited By ~ 96

Author(s):

I A.P Parkin ◽

A G Sharpe ◽

D J Lydiate

Keyword(s):

Brassica Napus ◽

Genome Duplication ◽

Chromosomal Rearrangements ◽

Centric Fusion ◽

Linkage Groups ◽

Gross Chromosomal Rearrangements ◽

A Genome ◽

C Genome ◽

Homologous Locus ◽

Duplicate Loci

The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.Key words: genome evolution, Brassicaeae, polyploidy, homoeologous linkage groups.

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