An overview of current population genomics methods for the analysis of whole‐genome resequencing data in eukaryotes

YXC Bourgeois, BH Warren - Molecular Ecology, 2021 - Wiley Online Library
Characterizing the population history of a species and identifying loci underlying local
adaptation is crucial in functional ecology, evolutionary biology, conservation and …

Advancements and prospects of genome-wide association studies (GWAS) in maize

JH Sahito, H Zhang, ZGN Gishkori, C Ma… - International Journal of …, 2024 - mdpi.com
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling
intricate genotype–phenotype association across various species. Maize (Zea mays L.) …

Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii

J Yuan, S Jiang, J Jian, M Liu, Z Yue, J Xu, J Li… - Nature …, 2022 - nature.com
Tree peony (Paeonia ostii) is an economically important ornamental plant native to China. It
is also notable for its seed oil, which is abundant in unsaturated fatty acids such as α …

IIIVmrMLM: The R and C++ tools associated with 3VmrMLM, a comprehensive GWAS method for dissecting quantitative traits

M Li, YW Zhang, Y Xiang, MH Liu, YM Zhang - Molecular Plant, 2022 - cell.com
In most existing methods and softwares of genome-wide association studies (GWAS) for
detecting quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and …

N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection

T Zhang, C Shi, H Hu, Z Zhang, Z Wang, Z Chen… - Nature …, 2022 - nature.com
Molecular manipulation of susceptibility (S) genes that are antipodes to resistance (R) genes
has been adopted as an alternative strategy for controlling crop diseases. Here, we show …

Genome assembly of alfalfa cultivar zhongmu-4 and identification of SNPs associated with agronomic traits

R Long, F Zhang, Z Zhang, M Li, L Chen… - Genomics …, 2022 - academic.oup.com
Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high
nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking …

Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids

L Li, X Zheng, J Wang, X Zhang, X He, L Xiong… - Nature …, 2023 - nature.com
Genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice
due to additional nonadditive effects such as dominance. Here, we describe a pipeline …

Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications

P Ramu, RK Srivastava, A Sanyal, K Fengler… - Communications …, 2023 - nature.com
High-quality reference genome assemblies, representative of global heterotic patterns, offer
an ideal platform to accurately characterize and utilize genetic variation in the primary gene …

Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence

N Shanmugaraj, J Rajaraman, S Kale, R Kamal… - The Plant …, 2023 - academic.oup.com
Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as
barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of …

Genomic signatures of strawberry domestication and diversification

Z Fan, VM Whitaker - The Plant Cell, 2024 - academic.oup.com
Cultivated strawberry (Fragaria× ananassa) has a brief history of less than 300 yr, beginning
with the hybridization of octoploids Fragaria chiloensis and Fragaria virginiana. Here we …