Polyploidy before and after domestication of crop species

T Akagi, K Jung, K Masuda, KK Shimizu - Current Opinion in Plant Biology, 2022 - Elsevier
Recent advances in the genomics of polyploid species answer some of the long-standing
questions about the role of polyploidy in crop species. Here, we summarize the current …

A roadmap for research in octoploid strawberry

VM Whitaker, SJ Knapp, MA Hardigan… - Horticulture …, 2020 - academic.oup.com
The cultivated strawberry (Fragaria× ananassa) is an allo-octoploid species, originating
nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry …

Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species

LM Zingaretti, SA Gezan, LFV Ferrão… - Frontiers in plant …, 2020 - frontiersin.org
Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates
are predicted using genome wide marker information. Although numerous examples of GP …

Genome‐wide association of volatiles reveals candidate loci for blueberry flavor

LFV Ferrão, TS Johnson, J Benevenuto… - New …, 2020 - Wiley Online Library
Plants produce a range of volatile organic compounds (VOCs), some of which are perceived
by the human olfactory system, contributing to a myriad flavors. Despite the importance of …

A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.)

FZ Barreto, JRBF Rosa, TWA Balsalobre, MM Pastina… - PLoS …, 2019 - journals.plos.org
Sugarcane (Saccharum spp.) has a complex genome with variable ploidy and frequent
aneuploidy, which hampers the understanding of phenotype and genotype relations …

polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids

LV Clark, AE Lipka, EJ Sacks - G3: Genes, Genomes, Genetics, 2019 - academic.oup.com
Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and
restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates …

Impact of whole-genome duplications on structural variant evolution in Cochlearia

T Hämälä, C Moore, L Cowan, M Carlile… - Nature …, 2024 - nature.com
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote
evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding …

In the name of the rose: a roadmap for rose research in the genome era

MJM Smulders, P Arens, PM Bourke… - Horticulture …, 2019 - academic.oup.com
The recent completion of the rose genome sequence is not the end of a process, but rather a
starting point that opens up a whole set of new and exciting activities. Next to a high-quality …

Meiosis in polyploids and implications for genetic mapping: a review

NR Soares, M Mollinari, GK Oliveira, GS Pereira… - Genes, 2021 - mdpi.com
Plant cytogenetic studies have provided essential knowledge on chromosome behavior
during meiosis, contributing to our understanding of this complex process. In this review, we …

Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy

V Shastry, PE Adams, D Lindtke… - Molecular ecology …, 2021 - Wiley Online Library
Non‐random mating among individuals can lead to spatial clustering of genetically similar
individuals and population stratification. This deviation from panmixia is commonly observed …