scholarly journals A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

2021 ◽  
Author(s):  
Surbhi Grewal ◽  
Benedict Coombes ◽  
Ryan Joynson ◽  
Anthony Hall ◽  
John Fellers ◽  
...  
Keyword(s):  
Doubled Haploid ◽  
Wild Species ◽  
Wheat Chromosome ◽  
Single Copy ◽  
Introgression Lines ◽  
Wheat Genome ◽  
Wild Relative ◽  
Novel Approach ◽  
Breeding Programmes ◽  
Kasp Markers

Many wild relative species are being used in pre-breeding programmes to increase the genetic diversity of wheat. Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterise wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based KASP markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and PCR-amplicon-based sequencing of the wild species. But chromosome-specific KASPs assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum and development of a SNP discovery pipeline that generated ~38,000 SNPs in single-copy wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as functional. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.

scholarly journals Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome-specific KASP genotyping assays

2019 ◽  
Author(s):  
Surbhi Grewal ◽  
Stella Hubbart-Edwards ◽  
Caiyun Yang ◽  
Urmila Devi ◽  
Lauren Baker ◽  
...  
Keyword(s):  
Cost Effective ◽  
Single Copy ◽  
Rapid Identification ◽  
Wild Relatives ◽  
Introgression Lines ◽  
Wheat Genome ◽  
Wild Relative ◽  
Backcross Population ◽  
Biotic Stresses ◽  
Specific Pcr

SummaryFor future food security it is important that wheat, one of the most widely consumed crops in the world, can survive the threat of abiotic and biotic stresses. New genetic variation is currently being introduced into wheat through introgressions from its wild relatives. For trait discovery, it is necessary that each introgression is homozygous and hence stable. Breeding programs rely on efficient genotyping platforms for marker-assisted selection (MAS). Recently, single nucleotide polymorphism (SNP) based markers have been made available on high-throughput Axiom® SNP genotyping arrays. However, these arrays are inflexible in their design and sample numbers, making their use unsuitable for long-term MAS. SNPs can potentially be converted into Kompetitive allele-specific PCR (KASP™) assays which are comparatively cost-effective and efficient for low-density genotyping of introgression lines. However, due to the polyploid nature of wheat, KASP assays for homoeologous SNPs can have difficulty in distinguishing between heterozygous and homozygous hybrid lines in a backcross population. To identify co-dominant SNPs, that can differentiate between heterozygotes and homozygotes, we PCR-amplified and sequenced genomic DNA from potential single-copy regions of the wheat genome and compared them to orthologous copies from different wild relatives. A panel of 620 chromosome-specific KASP assays have been developed that allow rapid detection of wild relative segments and provide information on their homozygosity and site of introgression in the wheat genome. A set of 90 chromosome-nonspecific assays was also produced that can be used for genotyping introgression lines. These multipurpose KASP assays represent a powerful tool for wheat breeders worldwide.

scholarly journals Generation of Doubled Haploid Wheat-Triticum urartu Introgression Lines and Their Characterisation Using Chromosome-Specific KASP Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Surbhi Grewal ◽  
Veronica Guwela ◽  
Claire Newell ◽  
Cai-yun Yang ◽  
Stephen Ashling ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Bread Wheat ◽  
Doubled Haploid ◽  
Agronomic Traits ◽  
Introgression Lines ◽  
Wheat Varieties ◽  
Genotyping Array ◽  
Dh Lines ◽  
Stable Transmission ◽  
Kasp Markers

Wheat is one of the most important food and protein sources in the world and although, in recent years wheat breeders have achieved yield gains, they are not sufficient to meet the demands of an ever-growing population. Development of high yielding wheat varieties, resilient to abiotic and biotic stress resulting from climate change, has been limited by wheat’s narrow genetic base. In contrast to wheat, the wild relatives of wheat provide a vast reservoir of genetic variation for most, if not all, agronomic traits. Previous studies by the authors have shown the transfer of genetic variation from T. urartu into bread wheat. However, before the introgression lines can be exploited for trait analysis, they are required to have stable transmission of the introgressions to the next generation. In this work, we describe the generation of 86 doubled haploid (DH) wheat-T. urartu introgression lines that carry homozygous introgressions which are stably inherited. The DH lines were characterised using the Axiom® Wheat Relative Genotyping Array and 151 KASP markers to identify 65 unique T. urartu introgressions in a bread wheat background. DH production has helped accelerate the breeding process and facilitated the early release of homozygous wheat-T. urartu introgression lines. Together with the KASP markers, this valuable resource could greatly advance identification of beneficial alleles that can be used in wheat improvement.

Doubled haploid production in maize under Sub-montane Himalayan conditions using R1-nj-based haploid inducer TAILP1

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
R. K Khulbe ◽  
A. Pattanayak ◽  
Lakshmi Kant ◽  
G. S. Bisht ◽  
M. C. Pant ◽  
...  
Keyword(s):  
Doubled Haploid ◽  
Sweet Corn ◽  
Haploid Induction ◽  
Maize Breeding ◽  
Line Production ◽  
Haploid Inducer ◽  
Breeding Programmes ◽  
Source Populations ◽  
Developmental Phases

The use of in vivo haploid induction system makes the doubled haploid (DH) technology easier to adopt for the conventional maize breeders. However, despite having played an important role in the initial developmental phases of DH technology, Indian maize research has yet to harvest its benefits. Haploid Inducer Lines (HILs) developed by CIMMYT are being widely used in maize breeding programmes in many countries including India. There, however, is no published information on the efficiency of DH line production using CIMMYT HILs in Indian maize breeding programmes. In the present study, the efficiency of DH production using CIMMYT’s tropically adapted inducer line TAILP1 was investigated with eight source populations including two of sweet corn. The average haploid induction rate (HIR) of TAILP1 was 5.48% with a range of 2.01 to 10.03%. Efficiency of DH production ranged from 0.14 to 1.87% for different source populations with an average of 1.07%. The information generated will be useful for maize breeders intending to use DH technology for accelerated development of completely homozygous lines.

Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1923-1933 ◽  
Author(s):  
Lorinda K Anderson ◽  
Naser Salameh ◽  
Hank W Bass ◽  
Lisa C Harper ◽  
W Z Cande ◽  
...  
Keyword(s):  
Genetic Linkage ◽  
Chromosome Structure ◽  
Single Copy ◽  
Chromosome 9 ◽  
Linkage Maps ◽  
Cytogenetic Map ◽  
Recombination Nodules ◽  
Novel Approach ◽  
Genetic Linkage Maps ◽  
High Degree

Abstract Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.

Comparison of fatty acid composition of oil from original and regenerated populations of wild Helianthus species

2014 ◽  
Vol 13 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Gerald J. Seiler
Keyword(s):  
Fatty Acids ◽  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Wild Species ◽  
Oil Quality ◽  
Wild Sunflower ◽  
Breeding Programmes ◽  
Precise Relationship ◽  
Germplasm Accessions

Monitoring and protecting germplasm in genebanks using in situ collections while preserving its original genetic integrity is a priority of germplasm curation. Many germplasm accessions need to be regenerated due to their demand and/or seed condition. The regeneration of wild Helianthus (sunflower) species poses several challenges due to the diversity of 53 wild species. Fatty acid composition of sunflower oil is an important quality factor for the crop. Since oil quality is environmentally influenced, and evaluation of this trait is usually performed on oil from achenes from the original accessions of wild sunflower species, we conducted a study on 72 accessions of eight annual and four perennial taxa of wild sunflower species to compare the oil quality of the original accessions and those regenerated for genebank maintenance. The results showed that the fatty acid composition profiles of achenes from the original and regenerated accessions are not the same. It seems that selection for specific fatty acids in several species will require the analysis of both populations to identify germplasm accessions for use in breeding programmes. It should be borne in mind that accessions of wild species are open-pollinated segregating populations, so one would expect some variability in each succeeding generation. While there may be differences between the original and regenerated accessions, the interrelationships of fatty acids are generally similar in wild and cultivated sunflower species, so there should be no detrimental effects on oil quality when using the wild species for other traits. As more regenerated accessions become available, a more precise relationship between the original and regenerated accessions should emerge.

The high fruit soluble sugar content in wild Lycopersicon species and their hybrids with cultivars depends on sucrose import during ripening rather than on sucrose metabolism

2006 ◽  
Vol 33 (3) ◽  
pp. 279 ◽  
Author(s):  
María E. Balibrea ◽  
Cristina Martínez-Andújar ◽  
Jesús Cuartero ◽  
María C. Bolarín ◽  
Francisco Pérez-Alfocea
Keyword(s):  
Wild Species ◽  
Sugar Content ◽  
Soluble Sugar ◽  
Sucrose Metabolism ◽  
F1 Hybrids ◽  
Metabolic Parameter ◽  
Wild Relative ◽  
Soluble Sugar Content ◽  
Total Soluble Sugar ◽  
In The Wild

Soluble sugar content has been studied in relation to sucrose metabolism in the hexose-accumulating cultivated tomato Lycopersicon esculentum Mill, the wild relative species Lycopersicon cheesmanii Riley, in the sucrose-accumulating wild relative species Lycopersicon chmielewskii Rick, Kesicky, Fobes & Holle. and in two hexose-accumulating interspecific F1 hybrids (L. esculentum × L. cheesmanii; L. esculentum × L. chmielewskii), cultivated under two irrigation regimes (control: EC = 2.1 and saline: EC = 8.4 dS m–1). Under control conditions the total soluble sugar content (as hexose equivalents) in the ripe fruits of L. cheesmanii was 3-fold higher than in L. esculentum, while L. chmielewskii and both F1 hybrids contained twice as much as the cultivar. With the exception of L. esculentum × L. cheesmanii, salinity increased the sugar content by 1.3 (wild species) and 1.7 times (cultivar and L. esculentum × L. chmielewskii) with respect to control fruits. Wild germplasm or salinity provided two different mechanisms for the increases in fruit sugar content. The hexoses accumulated in ripe fruits were strongly influenced by those accumulated at the start of ripening, but the hydrolysed starch before start of ripening only partially explained the final hexose levels and especially the increase under salinity. The early cell wall acid invertase and the late neutral invertase activities appeared to be related to the amount of hexoses accumulated in ripe fruits. However, no metabolic parameter was positively related to the amount of sugar accumulated (including sucrose). The major differences between genotypes appeared in ripe fruits, in which up to 50% of the total amount of sugars accumulated in the wild species (mainly in L. cheesmanii) and hybrids cannot be explained by the sugars accumulated and the starch hydrolysed before the start of ripening stage. As a consequence, the higher fruit quality of the wild species compared with L. esculentum may depend more on the continuation of sucrose import during ripening than on osmotic or metabolic particularities such as the hexose / sucrose-accumulator character or specific enzyme activities.

Karyotype stability in the genus Phaseolus evidenced by the comparative mapping of the wild species Phaseolus microcarpus

Genome ◽  
2013 ◽  
Vol 56 (6) ◽  
pp. 335-343 ◽  
Author(s):  
Artur Fonsêca ◽  
Andrea Pedrosa-Harand
Keyword(s):  
Common Bean ◽  
Wild Species ◽  
5S Rdna ◽  
Single Copy ◽  
Rdna Site ◽  
Phylogenetic Distance ◽  
Bacterial Artificial Chromosomes ◽  
Telomeric Dna ◽  
Artificial Chromosomes ◽  
Rdna Sites

The genus Phaseolus L. (Fabaceae) is monophyletic and comprises approximately 75 species distributed into two principal clades. The five cultivated species, including the common bean (Phaseolus vulgaris), were placed in clade B. Clade A comprises only wild species, with more limited distribution. In the present work, bacterial artificial chromosomes (BACs) previously mapped in common bean (2n = 22) were used as probes in fluorescent in situ hybridization (FISH) in this comparative study of Phaseolus microcarpus (2n = 22), a species from clade A. We also analyzed the chromomycin A3 (CMA)/4′,6-diamidino-2-phenylindole (DAPI) banding pattern and the localization of rDNA and telomeric DNA sites. The single 45S rDNA site from P. microcarpus was mapped to chromosome 6, showing conservation to the P. vulgaris homeolog. Of the two 5S rDNA sites identified in both species, only the site on chromosome 10 appeared conserved. In spite of the phylogenetic distance between the two species, all of the single-copy BACs demonstrated conservation of synteny. However, four collinearity breaks were observed, probably caused by para- and pericentric inversions. Some variation in the repetitive fraction of the genome was also observed. Thus, a broader analysis of the genus confirms that few, rare inversions seem to represent the main karyotype changes during the evolution of this genus.

scholarly journals Applicability of chromosome-specific SSR wheat markers for the introgression of Triticum urartu in durum wheat breeding programmes

2011 ◽  
Vol 9 (3) ◽  
pp. 439-444 ◽  
Author(s):  
C. Rodríguez-Suárez ◽  
M. C. Ramírez ◽  
A. Martín ◽  
S. G. Atienza
Keyword(s):  
Durum Wheat ◽  
Triticum Turgidum ◽  
Crop Improvement ◽  
Wheat Chromosome ◽  
Wheat Breeding ◽  
Triticum Urartu ◽  
Founder Line ◽  
A Genome ◽  
Breeding Programmes ◽  
Novel Alleles

Triticum urartu, the A-genome donor of tetraploid and hexaploid wheats, is a potential source of novel alleles for crop improvement. A fertile amphiploid between T. urartu (2n = 2x = 14; AuAu) and durum wheat cv ‘Yavaros’ (Triticum turgidum ssp. durum; 2n = 4x = 28, AABB) was obtained as a first step to making the genetic variability of the wild ancestor available to durum wheat breeding. The amphiploid was backcrossed with ‘Yavaros’ and the offspring from this cross was selfed. A plant from this progeny (founder line) with 28 chromosomes and active x and y subunits of the Glu-A1 locus of T. urartu was selfed, which resulted in the obtaining of 98 pre-introgression lines (pre-ILs). In this work, a set of 78 wheat chromosome-specific microsatellite markers (simple sequence repeats, SSR), uniformly distributed over the A genome, was used for marker-assisted selection of T. urartu in a durum wheat background. A total of 57 SSRs allowed a clear discrimination between T. urartu and ‘Yavaros’. This set of markers was further used for characterizing the pre-ILs, identifying and defining the T. urartu introgressed regions. The applicability of these markers is discussed.

scholarly journals Tradition, quality and biotechnology in Hungarian spice pepper ( Capsicum annuum L.) breeding

2010 ◽  
Vol 58 (3) ◽  
pp. 259-266 ◽  
Author(s):  
J. Pauk ◽  
C. Lantos ◽  
G. Somogyi ◽  
P. Vági ◽  
Z. Ábrahám Táborosi ◽  
...  
Keyword(s):  
Doubled Haploid ◽  
Microspore Culture ◽  
Isolated Microspore Culture ◽  
Culture Methods ◽  
Culture Techniques ◽  
New Genotype ◽  
Breeding Programmes ◽  
History Of ◽  
Dh Lines ◽  
Two Hybrid

Spice pepper production has a history of almost 300 years in the southern part of Hungary. In this study the results of two biotechnological improvements are summarized. Anther and isolated microspore culture techniques were improved to release haploid and doubled haploid (DH) lines for spice pepper breeding. Both the anther and isolated microspore culture methods were successfully used in spice pepper haploid production. Microspore culture-derived structures were analysed to identify their different parts. Green plantlets were regenerated from embryos derived from both anther and microspore cultures. Their doubled haploid analogues were integrated into Hungarian spice pepper hybrid seed breeding programmes. One hybrid, Sláger, was released as a new genotype for spice pepper production in 2008 and two hybrid candidates (Délibáb and Bolero) are now being tested in official trials.

Development of a set of compensating Triticum aestivum – Dasypyrum villosum Robertsonian translocation lines

Genome ◽  
2011 ◽  
Vol 54 (10) ◽  
pp. 836-844 ◽  
Author(s):  
Cheng Liu ◽  
Lili Qi ◽  
Wenxuan Liu ◽  
Wanchun Zhao ◽  
Jamie Wilson ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
Kernel Weight ◽  
Wild Relative ◽  
Dasypyrum Villosum ◽  
Robertsonian Translocations ◽  
Wheat Improvement ◽  
Improvement Programs ◽  
Hundred Kernel Weight

Dasypyrum villosum (L.) Candargy, a wild relative of bread wheat ( Triticum aestivum L.), is the source of many agronomically important genes for wheat improvement. Production of compensating Robertsonian translocations (cRobTs), consisting of D. villosum chromosome arms translocated to homoeologous wheat chromosome arms, is one of the initial steps in exploiting this variation. The cRobTs for D. villosum chromosomes 1V, 4V, and 6V have been reported previously. Here we report attempted cRobTs for wheat – D. villosum chromosome combinations 2D/2V, 3D/3V, 5D/5V, and 7D/7V. The cRobTs for all D. villosum chromosomes were recovered except for the 2VS and 5VL arms. As was the case with the 6D/6V combination, no cRobTs involving 2D/2V chromosomes were recovered; instead, cRobT T2BS·2VL involving a nontargeted chromosome was recovered. All cRobTs are fertile, although the level of spike fertility and hundred kernel weight (HKW) varied among the lines. The set of cRobTs involving 12 of the 14 D. villosum chromosomes will be useful in wheat improvement programs. In fact, among the already reported cRobTs, T6AL·6VS carrying the Pm21 gene is deployed in agriculture and many useful genes have been reported on other cRobTs including resistance to stem rust race UG99 on T6AS·6VL.

Sign in / Sign up

Export Citation Format

Share Document