Genomic approaches for studying crop evolution

Schreiber, Mona; Stein, Nils; Mascher, Martin

doi:10.1186/s13059-018-1528-8

Cited by 63 publications

(52 citation statements)

References 233 publications

(235 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genetic study of populations is a main approach for analysing crop evolution and domestication (Schreiber et al, 2018). The published cotton reference genomes of G. hirsutum and G. barbadense (Hu et al, 2019;Wang et al, 2019) have significantly contributed to our knowledge of cotton population genetics, and have allowed for the dissection of complex traits, in addition to uncovering domestication signatures and large-scale genetic variations (Wang et al, 2015;Wang et al, 2017;Ma et al, 2018;Wen et al, 2018;Wen et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

et al. 2020

View full text Add to dashboard Cite

SUMMARY The two new world tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, are cultivated worldwide and are characterised by a high yield and superior fibre quality, respectively. Historical genetic introgression has been reported between them; however, the existence of introgression and its genetic effects on agronomic traits remain unclear with regard to independent breeding of G. hirsutum (Upland cotton) and G. barbadense (Pima cotton) elite cultivars. We collected 159 G. hirsutum and 70 G. barbadense cultivars developed in Xinjiang, China, along with 30 semi‐wild accessions of G. hirsutum, to perform interspecific introgression tests, intraspecific selection analyses and genome‐wide association studies (GWAS) with fibre quality and yield component traits in multiple environments. In total, we identified seven interspecific introgression events and 52 selective sweep loci in G. hirsutum, as well as 17 interspecific introgression events and 19 selective sweep loci in G. barbadense. Correlation tests between agronomic traits and introgressions showed that introgression loci were mutually beneficial for the improvement of fibre quality and yield traits in both species. In addition, the phenotypic effects of four interspecific introgression events could be detected by intraspecific GWAS, with Gb_INT13 significantly improving fibre yield in G. barbadense. The present study describes the landscape of genetic introgression and selection between the two species, and highlights the genetic effects of introgression among populations, which can be used for future improvement of fibre yield and quality in G. barbadense and G. hirsutum, respectively.

show abstract

Section: Introductionmentioning

confidence: 99%

High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The last few years have seen a tremendous advance in plant genomic sciences driven by technologies such as long read PacBio and lately Oxford Nanopore sequencing (Bolger et al , 2019) as well as new technologies to obtain long range structural information such as optical mapping and Hi-C based information (Schreiber, Stein and Mascher, 2018) . Indeed, it has been shown that these technological advances can be used to get (near) chromosome scale assemblies of sub-Gigabase genomes (Belser et al , 2018) and that they are particularly useful to unravel the genomes of wild species which are close relatives of important crops providing information about exotic germplasm and its use (Wu et al , 2018) .…”

Section: Discussionmentioning

confidence: 99%

ASolanum lycopersicoidesreference genome facilitates biological discovery in tomato

Powell¹,

Courtney

Schmidt

et al. 2020

Preprint

View full text Add to dashboard Cite

SummaryWild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs). Despite the utility of these wild relatives and their associated ILs, limited finished genomes have been produced to aid genetic and genomic studies. We have generated a chromosome-scale genome assembly for Solanum lycopersicoides LA2951 using PacBio sequencing, Illumina, and Hi-C. We identified 37,938 genes based on Illumina and Isoseq and compared gene function to the available cultivated tomato genome resources, in addition to mapping the boundaries of the S. lycopersicoides introgressions in a set of cv. VF36 x LA2951 introgression lines (IL). The genome sequence and IL map will support the development of S. lycopersicoides as a model for studying fruit nutrient/quality, pathogen resistance, and environmental stress tolerance traits that we have identified in the IL population and are known to exist in S. lycopersicoides.

show abstract

“…Plants sometimes transmit somatic mutations to their descendants asexually or sexually (in case when flower buds developments in somatically mutated part of plant). Mutations create variations in the gene pool, and the less favorable (or deleterious) mutations are removed from the gene pool by natural selection, while more favorable (beneficial or advantageous) ones tend to accumulate, resulting in evolutionary change [6]. Irradiation has been successfully used for mutation breeding in various crops and ornamental plants [37] and has proven an adept means of encouraging the expression of recessive genes and producing new genetic variations [23,[36][37][38].…”

Section: Introductionmentioning

confidence: 99%

X-ray Induced Genetic Variability in <i>Amaranthus hybridus</i> L. and Analysis of Variants Using Morphological and Random Amplified Polymorphic DNA Data

Nwankwo¹,

Omosun²,

Edeoga³

et al. 2019

IJGG

View full text Add to dashboard Cite

Amaranthus hybridus L. is an important vegetable in Nigeria, grown mainly for its highly nutritious leaves. In a bid to explore the possibility of increasing the infra-specific diversity of the crop, we induced three accessions of A. hybridus from Anambra State, Nigeria with x-ray particles using various concentration levels. The experimental layout composed a 5 x 3 x 3 Randomized Complete Block Design arrangement, with treatment levels: 1 MGY, 2 MGY, 4 MGY, and 6 MGY, selectively allotted to the different accession based on a preliminary dosimetry test. Morphological data were recorded and subsequently leaves samples subjected to Deoxyribonucleic Acid (DNA) extraction and Random Amplified Polymorphic DNA (RAPD) analysis. The results show that except for inflorescence weight, other morphological data were not statistically significant. However, RAPD techniques identify some variations induced by x-ray particles on the different accessions. Ogbunike accession irradiated with 4 MGY appears to show the optimum concentration of x-ray particles required to induce genetic variability in A. hybridus. These findings are of paramount importance to plant breeders, whose primary tool is to identify variations to produce better yielding varieties.

show abstract

Genomic approaches for studying crop evolution

Cited by 63 publications

References 233 publications

High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

ASolanum lycopersicoidesreference genome facilitates biological discovery in tomato

X-ray Induced Genetic Variability in <i>Amaranthus hybridus</i> L. and Analysis of Variants Using Morphological and Random Amplified Polymorphic DNA Data

Contact Info

Product

Resources

About

Genomic approaches for studying crop evolution

Cited by 63 publications

References 233 publications

High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

High‐density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China

ASolanum lycopersicoidesreference genome facilitates biological discovery in tomato

X-ray Induced Genetic Variability in &lt;i&gt;Amaranthus hybridus&lt;/i&gt; L. and Analysis of Variants Using Morphological and Random Amplified Polymorphic DNA Data

Contact Info

Product

Resources

About

X-ray Induced Genetic Variability in <i>Amaranthus hybridus</i> L. and Analysis of Variants Using Morphological and Random Amplified Polymorphic DNA Data