Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

QTL Mapping Low-Temperature Germination Ability in the Maize IBM Syn10 DH Population

(2022) Qinghui Han et al.   Plants-Basel

Detection of quantitative trait loci (QTL) associated with spring regrowth in alfalfa (Medicago sativa L.)

(2022) Xue-qian JIANG et al.   Journal of Integrative Agriculture

Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis

(2021) Dongmei Ma et al.   BMC PLANT BIOLOGY

From genes to networks: The genetic control of leaf development

(2021) Hongfeng Wang et al.   Journal of Integrative Plant Biology

Transcriptional profiling of two contrasting genotypes uncovers molecular mechanisms underlying salt tolerance in alfalfa

(2021) Rakesh Kaundal et al.   Scientific Reports

Identification of Differential Drought Response Mechanisms in Medicago sativa subsp. sativa and falcata through Comparative Assessments at the Physiological, Biochemical, and Transcriptional Levels

(2021) Stacy D. Singer et al.   Plants-Basel

Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

(2020) Yixuan Li et al.   BMC PLANT BIOLOGY

Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley

(2020) Behnam Derakhshani et al.   PLoS One

Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa

(2020) Haitao Chen et al.   Nature Communications

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq

(2020) Lei Lei et al.   Rice

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance

(2020) Biruk A. Feyissa et al.   BMC GENOMICS

Construction of high‐density genetic linkage map and mapping quantitative trait loci (QTL) for flowering time in autotetraploid alfalfa ( Medicago sativa L.) using genotyping by sequencing

(2020) Fan Zhang et al.   Plant Genome

Enhanced Expression of QTL qLL9/DEP1 Facilitates the Improvement of Leaf Morphology and Grain Yield in Rice

(2019) Xue Fu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

QTL fine-mapping of soybean (Glycine max L.) leaf type associated traits in two RILs populations

(2019) Liang Wang et al.   BMC GENOMICS

High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq

(2019) Fan Zhang et al.   BMC PLANT BIOLOGY

Quantitative trait loci mapping of leaf rust resistance in tetraploid alfalfa

(2019) Laxman Adhikari et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

QTL mapping for leaf morphology traits in a large maize-teosinte population

(2019) Yuhua Fu et al.   MOLECULAR BREEDING

QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.)

(2019) Laxman Adhikari et al.   BMC PLANT BIOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Molecular networks regulating the cell division during leaf growth in Arabidopsis

(2019) Jasmien Vercruysse et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genetic Engineering for Global Food Security: Photosynthesis and Biofortification

(2019) Andrew John Simkin   Plants-Basel

OUP accepted manuscript

(2018)   BIOINFORMATICS

Comparative analysis of alfalfa (Medicago sativa L.) leaf transcriptomes reveals genotype-specific salt tolerance mechanisms

(2018) Yunting Lei et al.   BMC PLANT BIOLOGY

Identification and Fine-Mapping of a Major Maize Leaf Width QTL in a Re-sequenced Large Recombinant Inbred Lines Population

(2018) Baobao Wang et al.   Frontiers in Plant Science

A SNP-Based Linkage Map Revealed QTLs for Resistance to Early and Late Leaf Spot Diseases in Peanut (Arachis hypogaea L.)

(2018) Suoyi Han et al.   Frontiers in Plant Science

Dissecting Key Adaptation Traits in the Polyploid Perennial Medicago sativa Using GBS-SNP Mapping

(2018) Laxman Adhikari et al.   Frontiers in Plant Science

TissueEnrich: Tissue-specific gene enrichment analysis

(2018) Ashish Jain et al.   BIOINFORMATICS

Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq

(2018) Qiming Cheng et al.   BMC GENOMICS

Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L.

(2018) Qiang Zhou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Current Advances in Molecular Basis and Mechanisms Regulating Leaf Morphology in Rice

(2018) Peizhou Xu et al.   Frontiers in Plant Science

QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing

(2018) Yuanting Zheng et al.   Frontiers in Genetics

Nodulation response to molybdenum supplementation in alfalfa and its correlation with root and shoot growth in low pH soil

(2017) Laxman Adhikari et al.   JOURNAL OF PLANT NUTRITION

Genetic dissection and validation of candidate genes for flag leaf size in rice (Oryza sativa L.)

(2017) Xinxin Tang et al.   THEORETICAL AND APPLIED GENETICS

Alteration in Auxin Homeostasis and Signaling by Overexpression Of PINOID Kinase Causes Leaf Growth Defects in Arabidopsis thaliana

(2017) Kumud Saini et al.   Frontiers in Plant Science

Genetic architecture of flag leaf length and width in rice (Oryza sativa L.) revealed by association mapping

(2016) Jiantao Wu et al.   Genes & Genomics

Forever Young: The Role of Ubiquitin Receptor DA1 and E3 Ligase BIG BROTHER in Controlling Leaf Growth and Development

(2016) Hannes Vanhaeren et al.   PLANT PHYSIOLOGY

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

(2016) Nicholas J. Schurch et al.   RNA

Identification of QTL underlying physiological and morphological traits of flag leaf in barley

(2015) Lipan Liu et al.   BMC GENETICS

The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies

(2015) Jamie A. O’Rourke et al.   BMC GENOMICS

QTLs for flag leaf size and their influence on yield-related traits in wheat (Triticum aestivum L.)

(2015) Xiaoli Fan et al.   MOLECULAR BREEDING

Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations

(2015) Shanshan Li et al.   PLoS One

Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.)

(2015) Beat Keller et al.   THEORETICAL AND APPLIED GENETICS

Detection of QTL for forage yield, lodging resistance and spring vigor traits in alfalfa (Medicago sativa L.)

(2014) Per McCord et al.   EUPHYTICA

Perception of root-derived peptides by shoot LRR-RKs mediates systemic N-demand signaling

(2014) R. Tabata et al.   SCIENCE

A Saturated Genetic Linkage Map of Autotetraploid Alfalfa ( Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome

(2014) Xuehui Li et al.   G3-Genes Genomes Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza)

(2013) R. Giuliani et al.   PLANT PHYSIOLOGY

Applied Genetics and Genomics in Alfalfa Breeding

(2012) Xuehui Li et al.   Agronomy-Basel

Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species

(2011) J. W. VAN OOIJEN   Genetics Research

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Increased Leaf Size: Different Means to an End

(2010) N. Gonzalez et al.   PLANT PHYSIOLOGY

Environmental Effects on Spatial and Temporal Patterns of Leaf and Root Growth

(2009) Achim Walter et al.   Annual Review of Plant Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS