Person:
Hearne, S.

Profile Picture
Email Address
Birth Date
Research Projects
Organizational Units
Job Title
Last Name
Hearne
First Name
S.
Name
Hearne, S.
ORCID ID
0000-0003-2015-2450

Filters

2016 - 20186
Reset filters

Settings

AGROVOC: GERMPLASM ×

Search Results

Now showing 1 - 6 of 6
  • Thumbnail Image
    Publication
  • Thumbnail Image
    Publication
  • Thumbnail Image
    Publication
  • Thumbnail Image
    Publication
  • Thumbnail Image
    Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts
    (Public Library of Science, 2017) Brandenburg, J.T.; Tristan Mary-Huard; Rigaill, G.; Hearne, S.; Corti, H.; Joets, J.; Vitte, C.; Charcosset, A.; Nicolas, S.; Tenaillon, M.I.
    Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans.
    Publication
  • Thumbnail Image
    The development of quality control genotyping approaches: a case study using elite maize lines
    (Public Library of Science, 2016) Jiafa Chen; Zavala Espinosa, C.; Ortega, N.; Petroli, C.; Franco, J.; Burgueño, J.; Costich, D.E.; Hearne, S.
    Quality control (QC) of germplasmidentity and purity is a critical component of breeding and conservation activities. SNP genotyping technologies and increased availability of markers provide the opportunity to employ genotyping as a low-cost and robust component of this QC. In the public sector available low-cost SNP QC genotypingmethods have been developed from a very limited panel ofmarkers of 1,000 to 1,500 markers without broad selection of the most informative SNPs. Selection of optimal SNPs and definition of appropriate germplasm sampling in addition to platform section impact on logistical and resource-use considerations for breeding and conservation applications when mainstreaming QC. In order to address these issues, we evaluated the selection and use of SNPs for QC applications from large DArTSeq data sets generated from CIMMYT maize inbred lines (CMLs). Two QC genotyping strategies were developed, the first is a “rapid QC”, employing a small number of SNPs to identify potential mislabeling of seed packages or plots, the second is a “broad QC”, employing a larger number of SNP, used to identify each germplasm entry and tomeasure heterogeneity. The optimal marker selection strategies combined the selection ofmarkers with high minor allele frequency, sampling of clustered SNP in proportion tomarker cluster distance and selecting markers thatmaintain a uniform genomic distribution. The rapid and broad QC SNP panels selected using this approach were further validated using blind test assessments of related re-generation samples. The influence of sampling within each line was evaluated. Sampling 192 individuals would result in close to 100% possibility of detecting a 5%contamination in the entry, and approximately a 98%probability to detect a 2%contamination of the line. These results provide a framework for the establishment of QC genotyping. A comparison of financial and time costs for use of these approaches across different platforms is discussed providing a framework for institutions involved inmaize conservation and breeding to assess the resource use effectiveness of QC genotyping. Application of these research findings, in combination with existing QC approaches, will ensure the regeneration, distribution and use in breeding of true to type inbred germplasm. These findings also provide an effective approach to optimize SNP selection for QC genotyping in other species.
    Publication