Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

MF Scott, O Ladejobi, S Amer, AR Bentley, J Biernaskie… - Heredity, 2020 - nature.com
Crop populations derived from experimental crosses enable the genetic dissection of
complex traits and support modern plant breeding. Among these, multi-parent populations …

Exploring and exploiting pan-genomics for crop improvement

Y Tao, X Zhao, E Mace, R Henry, D Jordan - Molecular plant, 2019 - cell.com
Genetic variation ranging from single-nucleotide polymorphisms to large structural variants
(SVs) can cause variation of gene content among individuals within the same species. There …

Graph pangenome captures missing heritability and empowers tomato breeding

Y Zhou, Z Zhang, Z Bao, H Li, Y Lyu, Y Zan, Y Wu… - Nature, 2022 - nature.com
Missing heritability in genome-wide association studies defines a major problem in genetic
analyses of complex biological traits,. The solution to this problem is to identify all causal …

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

L Gao, I Gonda, H Sun, Q Ma, K Bao, DM Tieman… - Nature …, 2019 - nature.com
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We
present a tomato pan-genome constructed using genome sequences of 725 …

Toward an evolved concept of landrace

F Casañas, J Simó, J Casals, J Prohens - Frontiers in plant science, 2017 - frontiersin.org
The term “landrace” has generally been defined as a cultivated, genetically heterogeneous
variety that has evolved in a certain ecogeographical area and is therefore adapted to the …

Trait discovery and editing in tomato

C Rothan, I Diouf, M Causse - The Plant Journal, 2019 - Wiley Online Library
Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a
major crop species that is the top ranked vegetable produced over the world. Tomato is also …

[HTML][HTML] Tackling the climate, biodiversity and pollution emergencies by making peace with nature 50 years after the Stockholm Conference

IA Baste, RT Watson - Global Environmental Change, 2022 - Elsevier
Today's increasingly unequal and resource intensive development model degrades and
surpasses Earth's finite capacity to sustain human well-being. Society must restore this …

Succinct de Bruijn graphs

A Bowe, T Onodera, K Sadakane, T Shibuya - International workshop on …, 2012 - Springer
We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers
in a DNA sequence of length N has m edges, it can be represented in 4 m+ o (m) bits. This is …

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

B Pucker, I Irisarri, J de Vries, B Xu - Quantitative Plant Biology, 2022 - cambridge.org
Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore
Technologies and Pacific Biosciences are offering competing long-read sequencing …

Advances in omics approaches for abiotic stress tolerance in tomato

J Chaudhary, P Khatri, P Singla, S Kumawat, A Kumari… - Biology, 2019 - mdpi.com
Tomato, one of the most important crops worldwide, has a high demand in the fresh fruit
market and processed food industries. Despite having considerably high productivity …