- Plant Breeding, Plant Science, Molecular Breeding, Bioinformatics, Molecular Biology, Plant Molecular Biology, and 16 moreAgricultural Biotechnology, Molecular Markers, Crop genetic diversity, Crop Diversity and Evolution, Microsatellite Markers, Molecular Diversity, Classical Breeding, Biotechnology, Genetics, Genomics, Plant biotechnology, Molecular Genetics, Plant breeding and genetics, Industrial Biotechnology, Next generation sequencing, and Transcription Factorsedit
New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC... more
New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million single nucleotide polymorphism (SNP) markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome-wide linkage disequilibrium (LD) decayed to r 2 = 0.1 at a physical distance of ~100 kb. Seven and four quantitative trait loci (QTL) were identified for MC and HC, respectively. Promising candidate genes identified include Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17, and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE. These genes have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal MC and HC composition for food and feed by genomic-based breeding.
A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq... more
A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 quantitative trait loci (QTL) for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48–73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8–14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.
Research Interests:
Research Interests:
Single nucleotide polymorphisms (SNPs) have rapidly become the molecular marker of choice in plant and animal association mapping (AM) studies. In this work, a genome-wide association study (GWAS) and candidate quantitative trait loci... more
Single nucleotide polymorphisms (SNPs)
have rapidly become the molecular marker of choice
in plant and animal association mapping (AM) studies.
In this work, a genome-wide association study
(GWAS) and candidate quantitative trait loci (cQTL)
approaches were used to identify SNP markers
associated with seed quality traits, in a Brassica napus
L. association panel composed of 89 adapted winter
oilseed rape accessions. Six seed quality traits (oil and
protein content, linolenic acid, total glucosinolates, hemicellulose and cellulose content) were evaluated in
two different locations for two seasons. For GWAS,
4025 SNP markers evenly distributed along the
B. napus genome were genotyped using a 6K Illumina
array platform. For cQTL, 100 SNP markers previously
discovered in genomic regions underlying seed
quality QTL were genotyped using a competitive
allele-specific PCR (KASPar). Analysis of the population
structure revealed the presence of two weakly
differentiated subpopulations (FST = 0.037), with
82 % of the pairwise kinship comparisons ranging
from 0 to 0.1. The GWAS approach resulted in the
identification of 17 and 5 significant associations for
seed glucosinolate content and seed hemicellulose
content, respectively. The cQTL approach identified 4
significant associations for seed glucosinolate content
and 6 significant associations for seed hemicellulose
content. The associated SNPs were consistently identified
across environments and were mapped to
previously reported QTL. These results illustrate the
suitability of AM to identify SNP markers associated
with seed quality traits in B. napus.
have rapidly become the molecular marker of choice
in plant and animal association mapping (AM) studies.
In this work, a genome-wide association study
(GWAS) and candidate quantitative trait loci (cQTL)
approaches were used to identify SNP markers
associated with seed quality traits, in a Brassica napus
L. association panel composed of 89 adapted winter
oilseed rape accessions. Six seed quality traits (oil and
protein content, linolenic acid, total glucosinolates, hemicellulose and cellulose content) were evaluated in
two different locations for two seasons. For GWAS,
4025 SNP markers evenly distributed along the
B. napus genome were genotyped using a 6K Illumina
array platform. For cQTL, 100 SNP markers previously
discovered in genomic regions underlying seed
quality QTL were genotyped using a competitive
allele-specific PCR (KASPar). Analysis of the population
structure revealed the presence of two weakly
differentiated subpopulations (FST = 0.037), with
82 % of the pairwise kinship comparisons ranging
from 0 to 0.1. The GWAS approach resulted in the
identification of 17 and 5 significant associations for
seed glucosinolate content and seed hemicellulose
content, respectively. The cQTL approach identified 4
significant associations for seed glucosinolate content
and 6 significant associations for seed hemicellulose
content. The associated SNPs were consistently identified
across environments and were mapped to
previously reported QTL. These results illustrate the
suitability of AM to identify SNP markers associated
with seed quality traits in B. napus.
Research Interests:
Aluminium toxicity in acid soils is the main limitation to crop production worldwide. In wheat (Triticum aestivum L.), the Al-activated malate transporter (TaALMT1) gene located on chromosome 4DL is associated with malate efflux and... more
Aluminium toxicity in acid soils is the main limitation to crop production worldwide. In wheat (Triticum aestivum L.), the Al-activated malate transporter (TaALMT1) gene located on chromosome 4DL is associated with malate efflux and Al-tolerance. To introgress Al-tolerance from the breeding line CAR3911 into the high yielding Al-sensitive cultivar Kumpa-INIA, phenotypic and molecular characterizations of gene/QTL underlying Al-tolerance in CAR3911 followed by marker-assisted backcrossing (MAS-BC) were undertaken. Al-tolerant backcross (BC) lines were selected using the functional marker ALMT1-4 designed immediately upstream of the TaALMT1 coding region. Foreground and background selections using ALMT1-4 and microsatellite markers were conducted. Linkage and sequence analyses suggest that the TaALMT1 gene could underly the Al-tolerance in CAR3911, possessing the same promoter type (V) as the Al-tolerant genotypes Carazinho and ET8. The MAS-BC strategy allowed the selection of Al-tolerant lines with the smallest introgressed region (6 cM) on 4D and the highest recurrent parent genome (RPG) (98 %) covering 2194 cM of the wheat genome. The homozygous BC3F2 line named Kumpa-INIA-TaALMT1 expressed a 3-fold higher
Al-tolerance than its isogenic line Kumpa-INIA at 40 μM Al in the hydroponic solution, and similar to CAR3911 and Carazinho. The MAS-BC strategy was successful for the introgression of the TaALMT1 gene into Kumpa-INIA in only three BC generations, shortening the breeding cycle to 24 months, which promises to increase wheat production and a greater yield stability in the acid soils of Southern Chile.
Al-tolerance than its isogenic line Kumpa-INIA at 40 μM Al in the hydroponic solution, and similar to CAR3911 and Carazinho. The MAS-BC strategy was successful for the introgression of the TaALMT1 gene into Kumpa-INIA in only three BC generations, shortening the breeding cycle to 24 months, which promises to increase wheat production and a greater yield stability in the acid soils of Southern Chile.
Research Interests:
Flax seed yield is a complex trait and result of the inter-relationship between many crop characteristics. Structural Equation Modelling (SEM) is a flexible statistical method used to determine the relationship between measured variables... more
Flax seed yield is a complex trait and result of the inter-relationship between many crop characteristics. Structural Equation Modelling (SEM) is a flexible statistical method used to determine the relationship between measured variables such as crop characteristics. Observed variables (crop phenology, canopy traits, yield and its components) were included in the structural equation models to determine how these crop characteristics related to seed yield in a phenotypically diverse collection of flax germplasm. Early season vigour measured by plant stand was positively associated with canopy light interception and greater seed yield. Plant height was also identified to have a significant positive effect on seed yield. Moreover, yield components, such as thousand seed weight, number of bolls (capsules) per unit area and boll weight were strongly and positively correlated to seed yield. Focusing on yield-related traits, canopy architecture and expansion and seed weight to breed for yield improvement in flax may be superior to targeting yield by itself.
Research Interests:
Pale flax (Linum bienne Mill.) is the wild progenitor of cultivated flax (Linum usitatissimum L.) and represents the primary gene pool to broaden its genetic base. Here, a collection of 125 pale flax accessions and the Canadian flax core... more
Pale flax (Linum bienne Mill.) is the wild
progenitor of cultivated flax (Linum usitatissimum L.)
and represents the primary gene pool to broaden its
genetic base. Here, a collection of 125 pale flax
accessions and the Canadian flax core collection of
407 accessions were genotyped using 112 genomewide
simple sequence repeat markers and phenotyped
for nine traits with the aim of conducting population
structure, molecular diversity and association mapping
analyses. The combined population structure
analysis identified two well-supported major groups corresponding to pale and cultivated flax. The L.
usitatissimum convar. crepitans accessions most
closely resembled its wild progenitor, both having
dehiscent capsules. The unbiased Nei’s genetic distance
(0.65) confirmed the strong genetic differentiation
between cultivated and pale flax. Similar levels
of genetic diversity were observed in both species,
albeit 430 (48 %) of pale flax alleles were unique, in
agreement with their high genetic differentiation.
Significant associations were identified for seven and
four traits in pale and cultivated flax, respectively.
Favorable alleles with potentially positive effect to
improve yield through yield components were identified
in pale flax. The allelic frequencies of markers
associated with domestication-related traits such as capsular dehiscence indicated directional selection
with the most common alleles in pale flax being absent
or rare in cultivated flax and vice versa. Our results
demonstrated that pale flax is a potential source of
novel variation to improve multiple traits in cultivated
flax and that association mapping is a suitable
approach to screening pale flax germplasm to identify
favorable quantitative trait locus alleles.
progenitor of cultivated flax (Linum usitatissimum L.)
and represents the primary gene pool to broaden its
genetic base. Here, a collection of 125 pale flax
accessions and the Canadian flax core collection of
407 accessions were genotyped using 112 genomewide
simple sequence repeat markers and phenotyped
for nine traits with the aim of conducting population
structure, molecular diversity and association mapping
analyses. The combined population structure
analysis identified two well-supported major groups corresponding to pale and cultivated flax. The L.
usitatissimum convar. crepitans accessions most
closely resembled its wild progenitor, both having
dehiscent capsules. The unbiased Nei’s genetic distance
(0.65) confirmed the strong genetic differentiation
between cultivated and pale flax. Similar levels
of genetic diversity were observed in both species,
albeit 430 (48 %) of pale flax alleles were unique, in
agreement with their high genetic differentiation.
Significant associations were identified for seven and
four traits in pale and cultivated flax, respectively.
Favorable alleles with potentially positive effect to
improve yield through yield components were identified
in pale flax. The allelic frequencies of markers
associated with domestication-related traits such as capsular dehiscence indicated directional selection
with the most common alleles in pale flax being absent
or rare in cultivated flax and vice versa. Our results
demonstrated that pale flax is a potential source of
novel variation to improve multiple traits in cultivated
flax and that association mapping is a suitable
approach to screening pale flax germplasm to identify
favorable quantitative trait locus alleles.
Research Interests:
To feed the predicted extra two billion people by 2050, crop production must increase on existing cultivated land at a rate that challenges our current capability. Acid soils and aluminium (Al3+) toxicity restrict productivity worldwide... more
To feed the predicted extra two billion people by 2050, crop production must increase on existing cultivated land at a rate that challenges our current capability. Acid soils and aluminium (Al3+) toxicity restrict productivity worldwide but also offer the greatest opportunity for increases in global food production. Our understanding of the physiology, genetic control and the identification of genomic regions underlying Al resistance in important staple crops has increased greatly over the past 20 years, enabling the application of molecular breeding. In this study, we report the application of an efficient marker-assisted backcrossing (MAB) strategy for the introgression of the HvAACT1 gene which confers Al resistance in barley (Hordeum vulgare L.). We conducted foreground and background selection using microsatellite (SSR) markers linked to HvAACT1 and SSR-based linkage maps, along with embryo rescue and a cost-effective DNA preparation method shortening the breeding cycle to ~18 months. The MAB strategy enabled the development of homozygous (BC3F2) Al-resistant lines with the smallest introgressed region and 98.7 % of the recurrent parent genome. The Al-resistant line yielded significantly more seeds (121 %) than its isogenic line in soil-based assays containing 12 % of Al saturation. This MAB strategy could be extended to other staple crops with similar molecular toolboxes, expanding their cultivation onto acid soils, and contributing to greater yield stability and food security, particularly in developing countries.
Research Interests:
Research Interests:
One of the major concerns in genetic characterization and breeding of cultivated flax is the lack of informative microsatellite markers (SSRs). In this regard, the development of SSRs using molecular methods might be time-consuming,... more
One of the major concerns in genetic characterization and breeding of cultivated flax is the lack of informative microsatellite markers (SSRs). In this regard, the development of SSRs using molecular methods might be time-consuming, laborious, and expensive. On the other hand, using bioinformatics to mine sequences in public databases enables a cost-effective discovery of SSRs. A total of 3,242 Linum usitatissimum genomic sequences were surveyed for the identification of SSRs. Among them, 118 non-redundant sequences containing repeats were selected for designing primers. The most abundant motifs were tri- (72.4%) and dinudeotide (16.6%), within which AGG/CCT and AG/CT were predominant. Primers were tested for polymorphism in 60 L. usitatissimum cultivars/accessions including 57 linseed and three fiber flax. Eighty-eight pairs gave amplifications within the expected size range while 60 pairs were found to be polymorphic. The mean number of alleles amplified per primer was 3.0 (range, 2–8; 180 total alleles). The mean polymorphism information content (PIC) value was 0.39 (range, 0.06–0.87), and the highest average PIC was observed in dinucleotide SSRs (0.41). The SSR data mining presented here demonstrates the usefulness of in silico development of microsatellites. These novel genomic SSR markers could be used in genetic diversity studies, the development of genetic linkage maps, quantitative trait loci mapping, association mapping, and marker-assisted selection.