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GrainGenes Reference Report: Watkins-2024

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Reference	Watkins-2024
Title	Harnessing Landrace Diversity Empowers Wheat Breeding for Climate Resilience
Journal	Nature
Year	2024
Remark	[ Hide all but 1 of 54 ] Supplemental Tables are listed below: S1. Germplasm descriptors of the 1051 accessions used in this study. S2a. Statistics of the Watkins and modern SNPs. S2b. Statistics of the insertions and deletion (InDels) identified in the Watkins accessions. S3. Number of SNP classified according to minor allele frequencies (MAF). S4. Location of SNPs in 1051 accessions and putative functional significance S5. The ADMIXTURE results of 828 landrace accessions (827 Watkins and Chinese Spring) from K=2 to K=9 S6. The geographical distribution of sequenced accessions and their assigned ancestral groups, AG1 to AG7, for the Watkins landraces and modern varieties. S7. The number and percentage of population-specific and shared variants, including SNPs, Indels, copy number variations (CNVs), haplotypes and haploblocks. S8. Estimates of copy number variations (CNVs) for high-confidence (HC) wheat genes (107,891 HC genes) across the Watkins landraces and modern varieties. S9. Estimation of copy number variations (CNVs) for a selection of 317 genes across the 1051 accessions included in this study (Curator Note, VCB, Used for gene/SNP curation) S10. The cumulative contribution of Watkins accessions to each modern cultivar based on the 1 Mb haplotypes and minimum landrace path approach. S11. Wheat HapMap. S12. Number and cumulative length of the Wheat HapMap haploblocks distributed across the 21 chromosomes and categorised based on haploblock size. S13. The chromosome position and frequency of start gain and start lost variants. S14. The location and frequency of stop gained and stop lost variants. S15. Description of the 13,902 genes which are invariant in modern varieties. S16. Description of the 306 genes without SNPs in Watkins landraces. S17. The frequency of SNPs within selected functional genes. S18. Number of trial sites/environments in which each of the traits were recorded in different years. S19. Number of years in which each traits was recorded in different trial sites/environments. S20. Details of Recombinant Inbred Line (RIL) populations with Watkins parent used in this study. S21. Detailed descriptions of traits for which phenotypic data was collected in this study. S22. Description of the 137 traits phenotyped in the Nested Association Mapping (NAM) and natural populations. S23. The summary of locations and years for RIL populations and NIL phenotyping. S24. Number of Quantitative Trait Loci (QTLs) and Marker Trait Associations (MTA) discovered for each trait in the Natural and NAM populations. S25. Details of 3,280 QTL identified in the Paragon x Watkins RIL populations. S26. Detailed information of the 1428 MTAs for 39 traits from Watkins natural population genome wide association studies (GWAS). (Curator Note, VCB, Used for GWAS-QTL curation) S27. Detailed information of the 3545 MTAs for 82 traits from the NAM GWAS. S28. Gene candidates located in the genomic intervals identified in the GWAS/NAM GWAS. S29. The haplotype frequency and distribution (in AG1-7 vs. modern) with the estimated genetic effects (favourable or unfavourable) for each of the 3,545 MTAs discovered from the NAM population. S30. The haplotype frequency and distribution (in AG1-7 vs. modern) with the estimated genetic effects (favourable or unfavourable) for each of the 1,428 MTAs discovered from the natural population. S31. The haplotype frequency and distribution (in AG1-7 vs. modern) with the estimated genetic effects (favourable or unfavourable) for each of the 344 prioritised MTAs (a subset of the 3,545 MTAs summarised in Supplementary Table 27) discovered from the NAM population. S32. The haplotype frequency and distribution (in AG1-7 vs. modern) with the estimated genetic effects (favourable or unfavourable) for each of the prioritised 161 MTAs (a subset of the 1,428 MTAs summarised in Supplementary Table 26) discovered from the natural population. S33. Number of haplotypes among ancestral groups for the three Nitrogen Use Efficiency (NUE) candidate genes identified on chromosome 5A. S34. Watkins yellow rust seedling resistance, natural population. S35. Watkins yellow rust seedling resistance, RILs. S36. Yellow rust QTLs discovered using Paragon x Watkins RIL populations in UK under field conditions. S37. Candidate CBF genes associated with frost resistance. S38. Classification of 20 CBF genes based on gene region SNPs and CNVs. S39. Degree of cold resistance of SNPs and CNVs based haplotypes. S40. The number of accessions carrying the CBF haplotypes based on SNPs and CNV in the seven ancestral groups and modern varieties S41. Validation of phenotypic effects. S42. RHT8 field experiments. S43. Phenotypic classification of critical recombinants at RHT8 locus. S44. Molecular marker used to fine map RHT8. S45. Genotypes of RHT8 recombinants. S46. Number and proportion of Watkins unique haplotypes in the most significant blocks among 577 MTAs for disease-related traits: yellow rust, stem rust, Septoria, and take-all. S47. Grain calcium concentration and grain weight of TILLING mutants of TraesCS5A02G543300 along with wild-type Cadenza. S48. Detailed information of 738 Near Isogenic Lines (NILs). S49. Number of tagSNPs on each chromosome and their distribution in 5 Mb windows. S50. Hexaploid wheat accessions used to test the haplotype tag SNPs. S51. Comparison of GWAS results using genotypic data from different sources. S52. Lines selected for designing novel genotyping probes for the TaNG array.
Author	Cheng S [ Show all 89 ]
Abstract	Breeding crops resilient to climate change is urgently needed to help ensure food security. A key challenge is to harness genetic diversity to optimise adaptation, yield, stress resilience and nutrition. We examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat, leaving five groups as previously untapped sources for breeding. This provides access to landrace-specific functional variations using structured germplasm, genotyping and informatics resources. Employing complementary genetic populations and approaches, we identified thousands of high-resolution quantitative trait loci (QTL) and significant marker-trait associations for major traits, revealing many Watkins-unique loci that can confer superior traits in modern wheat. Furthermore, we identified and functionally verified causative genes for climate-change adaptation, nutritional enhancement and resistance to wheat blast. Finally, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.
External Databases	https://doi.org/10.1101/2023.10.04.560903
Gene	1fehw3 (Triticum) [ Show all 237 ]
Locus	chr2A_158309883 [ Show all 2525 ]
QTL	AwnCol_PBI_b1990_Natural-1B [ Show all 4708 ]

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