Query (optional)   in Class  All Allele Author Colleague Collection Assembly Gene Gene Class Gene Product Germplasm Image Journal Keyword Library Locus Map Map Data Marker Pathology Polymorphism Probe Protein QTL Rearrangement Reference Sequence Species Trait Trait Study Two Point Data  

---

GrainGenes Reference Report: PLO-14:e0218562

[Submit comment/correction]

Reference	PLO-14:e0218562
Title	Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. var durum) collection
Journal	PLoS ONE
Year	2019
Volume	14
Author	Roncallo PF Beaufort V Larsen AO Dreisigacker S Echenique V
Abstract	The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.
External Databases	https://doi.org/10.1371/journal.pone.0218562
Locus	[ Hide all but 1 of 150 ] BS00005036 BS00005272 BS00010779 BS00019332 BS00003634 BS00014413 BS00020741 BS00004546 BS00005343 BS00003575 BS00004981 BS00020527 BS00086854 BS00095622 BS00010735 BS00022530 BS00003743 BS00022851 BS00108257 BS00022093 BS00077329 BS00022411 BS00010888 BS00012056 BS00023148 BS00004129 BS00003807 BS00004673 BS00004727 BS00003694 BS00013085 BS00009848 BS00014046 BS00014923 BS00005060 BS00004224 BS00004378 BS00012830 BS00004417 BS00015274 BS00004158 BS00005117 BS00012743 BS00018367 BS00018474 BS00003837 BS00016725 BS00003776 BS00005047 BS00016097 BS00014101 BS00009274 BS00012772 BS00082002 BS00094343 BS00066143 BS00010757 BS00075379 BS00005311 BS00003767 BS00026513 BS00017579 BS00077936 BS00009369 BS00066421 BS00004698 BS00004142 BS00006033 BS00015223 BS00005092 BS00012739 BS00018086 Lr47-2 BS00014199 BS00018848 BS00009510 BS00017136 BS00015653 BS00012587 BS00004070 BS00003756 BS00014897 BS00010442 BS00016166 BS00003580 AX-94391951 AX-94397585 AX-94397650 AX-94433842 AX-94434557 AX-94440438 AX-94441767 AX-94442444 AX-94442784 AX-94449276 AX-94460534 AX-94461977 AX-94470927 AX-94476297 AX-94481194 AX-94484634 AX-94503942 AX-94506228 AX-94509664 AX-94512544 AX-94518002 AX-94529131 AX-94534554 AX-94543706 AX-94545658 AX-94550243 AX-94592260 AX-94628292 AX-94637341 AX-94657189 AX-94664467 AX-94666389 AX-94669331 AX-94672308 AX-94679343 AX-94686717 AX-94721310 AX-94752691 AX-94759937 AX-94766462 AX-94770581 AX-94783957 AX-94804276 AX-94810852 AX-94849575 AX-94882276 AX-94898875 AX-94903804 AX-94946007 AX-94963184 AX-94965847 AX-94997523 AX-95019077 AX-95084685 AX-95101816 AX-95108145 AX-95113483 AX-95148754 AX-95183381 AX-95191949 AX-95208962 AX-95215205 AX-95222099 AX-95240270 AX-95257184
Probe	BS00005036_KASP [ Show all 85 ]
Sequence	BS00005036_KASP [ Show all 84 ]

GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture.