A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (<i>Medicago sativa</i> L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the <i>Medicago truncatula</i> Genome

Li, Xuehui; Wei, Yanling; Acharya, Ananta; Jiang, Qingzhen; Kang, Junmei; Brummer, E. Charles

doi:10.1534/g3.114.012245

Cited by 95 publications

(143 citation statements)

References 42 publications

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“…We also tested "diploidized models" or "pseudodiploid models" using the tetraploid genotype calling, as they are widely-used in polyploid analyses due to straightforward implementation in diploid software (Li et al, 2014b;Biazzi et al, 2017). This parameterization disregards the allele dosage and all heterozygotes are grouped into the same genotypic class, which is at the midpoint between the two homozygotes (Rosyara et al, 2016;Slater et al, 2016).…”

Section: Snp-trait Associations In Autotetraploid Blueberriesmentioning

confidence: 99%

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

et al. 2018

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Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries and identify candidate genes affecting phenotypic variation. We performed a genome-wide association study (GWAS) assuming diploid and tetraploid inheritance, encompassing distinct models of gene action (additive, general, different orders of allelic interaction, and the corresponding diploidized models). A total of 1,575 southern highbush blueberry individuals from a breeding population of 117 full-sib families were genotyped using sequence capture and next-generation sequencing, and evaluated for eight fruit-related traits. For the diploid allele calling, 77,496 SNPs were detected; while 80,591 SNPs were obtained in tetraploid, with a high degree of overlap (95%) between them. A linear mixed model that accounted for population and family structure was used for the GWAS analyses. By modeling tetraploid genotypes, we detected 15 SNPs significantly associated with five fruit-related traits. Alternatively, seven significant SNPs were detected for only two traits using diploid genotypes, with two SNPs overlapping with the tetraploid scenario. Our results showed that the importance of tetraploid models varied by trait and that the use of diploid models has hindered the detection of SNP-trait associations and, consequently, the genetic architecture of some commercially important traits in autotetraploid species. Furthermore, 14 SNPs co-localized with candidate genes, five of which lead to non-synonymous amino acid changes. The potential functional significance of these SNPs is discussed.

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Section: Snp-trait Associations In Autotetraploid Blueberriesmentioning

confidence: 99%

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

et al. 2018

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“…Therefore, many benefits of functional genomics and molecular breeding techniques are now accessible to forage crop breeders. Alfalfa, red clover, and white clover have described genetic linkage maps and partial genome sequences based on assembled contigs and scaffolds [51][52][53][54][55]. Contig mapping and gene annotation of these genomes has been aided by cDNA sequencing, and genomic synteny mapping using well defined legume genomes, such as M. truncatula [53,[55][56][57].…”

Section: The Potential Of Modern Genomic and Phenomic Tools To Develomentioning

confidence: 99%

“…Alfalfa, red clover, and white clover have described genetic linkage maps and partial genome sequences based on assembled contigs and scaffolds [51][52][53][54][55]. Contig mapping and gene annotation of these genomes has been aided by cDNA sequencing, and genomic synteny mapping using well defined legume genomes, such as M. truncatula [53,[55][56][57]. Given these genomic tools, modern breeding methods such as genotyping by sequencing (GBS), genome-wide association study (GWAS), marker assisted selection (MAS), and TILLING can be integrated into traditional trait selection pipelines [58].…”

Section: The Potential Of Modern Genomic and Phenomic Tools To Develomentioning

confidence: 99%

Diurnal Leaf Starch Content: An Orphan Trait in Forage Legumes

et al. 2017

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Abstract:Forage legumes have a relatively high biomass yield and crude protein content, but their grazed and harvested biomass lacks the high-energy carbohydrates required to meet the productivity potential of modern livestock breeds. Because of their low carbohydrate content, forage legume diets are typically supplemented with starch rich cereal grains or maize (Zea mays), leading to the disruption of local nutrient cycles. Although plant leaves were first reported to accumulate starch in a diurnal pattern over a century ago, leaf starch content has yet to be exploited as an agronomic trait in forage crops. Forage legumes such as red clover (Trifolium pratense) have the genetic potential to accumulate up to one third of their leaf dry mass as starch, but this starch is typically degraded at night to support nighttime growth and respiration. Even when diurnal accumulation is considered with regard to the time the crop is harvested, only limited gains are realized due to environmental effects and post-harvest losses from respiration. Here we present original data for starch metabolism in red clover and place it in the broader context of other forage legumes such as, white clover (T. repens), and alfalfa (Medicago sativa). We review the application of recent advances in molecular breeding, plant biology, and crop phenotyping, to forage legumes to improve and exploit a potentially valuable trait for sustainable ruminant livestock production.

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“…Recently a genotyping-by-sequencing (GBS) based linkage map for fall dormancy of tetraploid alfalfa was reported [91]. The linkage groups identified on autotetraploid M. sativa were mostly syntenous with M. truncatula.…”

Section: Genetic Control Of Dormancymentioning

confidence: 99%

Insights into Seasonal Dormancy of Perennial Herbaceous Forages

Adhikari¹,

Razar²,

Paudel³

et al. 2017

AJPS

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Seasonal dormancy is an adaptive mechanism where plants suspend growth and become physiologically inactive to avoid extreme environmental conditions. Environmental factors like temperature, photoperiod, nutrients, and soil moisture control plant growth and development through various complex molecular mechanisms. Crown and seed dormancy of plants are mostly influenced by day length and temperature. Genes and physiological pathways triggered by these two factors along with genotype variability are some targets to manipulate seasonal dormancy. There is genetic variation in the depth and duration of seasonal dormancy. Therefore, their genetic manipulation is possible. Manipulations of summer and fall dormancy are relatively easier compared to winter dormancy because plants require protection of their apical meristem from freezing temperatures and limited water supply. Genetic factors that regulate seed dormancy may also have regulatory role for seasonal dormancy of the maternal plants. Limited genetic and genomic information are available for seasonal dormancy in herbaceous perennial species. Knowledge of genes controlling seasonal dormancy of eudicots, forest trees, and horticultural crops could be interpolated to explore possible dormancy mechanisms in perennial forages. This study reviews current knowledge of seasonal dormancy of herbaceous forages emphasizing the genetic and physiological context that would be valuable to breeders and plant biologists to expand the production season of perennial species by developing non-dormant and semi-dormant cultivars.

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A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome

Cited by 95 publications

References 42 publications

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

Diurnal Leaf Starch Content: An Orphan Trait in Forage Legumes

Insights into Seasonal Dormancy of Perennial Herbaceous Forages

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