Rice is a staple crop for half the world's population, which is expected to grow by 3 billion
over the next 30 years. It is also a key model for studying the genomics of agroecosystems …

Salt stress reduces land and water productivity and contributes to poverty and food
insecurity. Increased salinization caused by human practices and climate change is …

Motivation Linkage disequilibrium (LD) decay is of great interest in population genetic
studies. However, no tool is available now to do LD decay analysis from variant call format …

The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than
half a century. The debates have focused on two leading hypotheses: a single domestication …

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries)
may facilitate our efforts towards further improvement. Here, we report the deep …

The genus Oryza is a model system for the study of molecular evolution over time scales
ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the …

Domestication is a co-evolutionary process that occurs when wild plants are brought into
cultivation by humans, leading to origin of new species and/or differentiated populations that …

Upland cotton (Gossypium hirsutum) is the most important natural fiber crop in the world.
The overall genetic diversity among cultivated species of cotton and the genetic changes …

Advances in DNA sequencing technology have sparked a genomics revolution, driving
breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from …

We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated
perennial crop, to address three ongoing mysteries about plant domestication. The first is the …