Agricultural genetics

  • Article
    | Open Access

    Unlike wild Vitis species, which produce either female or male flowers, modern grapevine cultivars form hermaphrodite flowers for self-pollination. Here, the authors report that the VviPLATZ1 (plant AT-rich sequence-and zinc-binding protein1) transcription factor functions in controlling female flower morphology determination.

    • Pat Iocco-Corena
    • , Jamila Chaïb
    •  & Harley M. Smith
  • Article
    | Open Access

    The genes underlying stripe rust host specificity between wheat and barley remain unknown. Here, the authors report that Rps6, Rps7 and Rps8 determine host species specificity in barley at different stages of the pathogen lifecycle and the barley powdery mildew immune receptor Mla8 and Rps7 are the same gene.

    • Jan Bettgenhaeuser
    • , Inmaculada Hernández-Pinzón
    •  & Matthew J. Moscou
  • Article
    | Open Access

    While multiple resistance-to-Phytophthora sojae loci/alleles have been mapped in soybean, many of them have become ineffective to newly evolved isolates. Here, the authors show that a 27.7-kb nucleotide-binding site-leucine-rich repeat gene confers broad-spectrum resistance to P. sojae in soybean.

    • Weidong Wang
    • , Liyang Chen
    •  & Jianxin Ma
  • Article
    | Open Access

    How soybean, a temperate origin crop, adapted to a tropical environment remains unclear. Here, the authors report Tof16, an ortholog of LHY, and the previously identified J locus, control soybean yield under short-day condition and loss of function of these two genes contributes to the adaptation to tropics.

    • Lidong Dong
    • , Chao Fang
    •  & Baohui Liu
  • Article
    | Open Access

    The genetic basis of low-temperature tolerance in maize is unclear. Here, the authors show that the type-A Response Regulator 1 (ZmRR1) and mitogen-activated protein kinase (MPK8) are positive and negative regulators of maize chilling tolerance, and ZmRR1 is phosphorylated by ZmMPK8 during cold treatment.

    • Rong Zeng
    • , Zhuoyang Li
    •  & Shuhua Yang
  • Article
    | Open Access

    To explore the nature of wild and cultivated mandarins, the authors carry out genomic analysis of diverse east Asian citrus. The discovery of a wild species Citrus ryukyuensis native to the Ryukyu islands and a new population of wild mainland Asian mandarin explains the origin and diversity of mandarins and their ability to reproduce apomictically.

    • Guohong Albert Wu
    • , Chikatoshi Sugimoto
    •  & Daniel S. Rokhsar
  • Article
    | Open Access

    Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.

    • John T. Lovell
    • , Nolan B. Bentley
    •  & Jennifer J. Randall
  • Article
    | Open Access

    The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.

    • Alexis Groppi
    • , Shuo Liu
    •  & Véronique Decroocq
  • Article
    | Open Access

    Longhua Shui Mi (LHSM) is a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. Here, the authors assemble the genome of LHSM and show convergent selection for sweetness yet divergent selection for acidity in eastern vs. western cultivars through population genomics analyses.

    • Yang Yu
    • , Jiantao Guan
    •  & Hua Xie
  • Article
    | Open Access

    The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.

    • Jianping Zhang
    • , Timothy C. Hewitt
    •  & Evans S. Lagudah
  • Article
    | Open Access

    In contrast to common bean, tepary bean is highly adapted to heat and drought. Here, the authors assemble the genomes of tepary bean landrace and wild accession, discuss the possible mechanism for resilience to heat stress, and reveal a reduced disease resistance gene repertoire.

    • Samira Mafi Moghaddam
    • , Atena Oladzad
    •  & Phillip E. McClean
  • Article
    | Open Access

    The genomic organization and origin of the avenacin biosynthetic gene cluster remain unknown. Here, the authors assemble the genome of diploid oat Avena strigosa, reveal the structure and organization of the consecutive genes, characterize the last two missing pathway steps, and investigate the origin of the pathway in cereals.

    • Yan Li
    • , Aymeric Leveau
    •  & Anne Osbourn
  • Article
    | Open Access

    The genus Miscanthus has great potential for bio-energy production due to its high biomass yield and strong stress resistance. Here, the authors report the genome assembly of the diploid M. lutarioriparius, showing it has an allotetraploid origin and an expanded number of genes in families related to stress resistance.

    • Jiashun Miao
    • , Qi Feng
    •  & Bin Han
  • Article
    | Open Access

    Studies of fruit quality traits in pears are lagging behind the other major fruit trees. Here, the authors conduct GWAS of fruit quality and phenological traits in a panel of 312 sand pear accessions using SNPs called from resequencing data, and reveal the involvement of a lignin formation-related protein in regulating stone cell development.

    • Ming-Yue Zhang
    • , Cheng Xue
    •  & Jun Wu
  • Article
    | Open Access

    The development of hybrid wheat cultivars is hampered by the lack of an effective way to control male fertility in breeding lines. Here, the authors report the identification of two restorer-of-fertility genes Rf1 and Rf3 that can restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility.

    • Joanna Melonek
    • , Jorge Duarte
    •  & Ian Small
  • Article
    | Open Access

    Winter wheat cultivar Forno harbors a race-specific leaf rust resistance locus Lr14a, but the causative gene is unknown. Here, the authors show that Lr14a encodes a membrane-localized protein containing ankyrin repeats and Lr14a-containing segments have been introgressed into the bread wheat gene pool multiple times.

    • Markus C. Kolodziej
    • , Jyoti Singla
    •  & Beat Keller
  • Article
    | Open Access

    The white pupae (wp) phenotype has been used for decades to selectively remove females of tephritid species in genetic sexing, but the determining gene is unknown. Here, the authors show that wp phenotype is produced by parallel mutations in a Major Facilitator Superfamily domain containing gene across multiple species.

    • Christopher M. Ward
    • , Roswitha A. Aumann
    •  & Marc F. Schetelig
  • Article
    | Open Access

    The accumulation of recombination events in selfing species may lead to a rapid fixation of both beneficial and deleterious mutations. Here, the authors resequence 781 soybean accessions, show purging of deleterious mutation during domestication, and report genome-wide associations for seed protein and oil traits.

    • Myung-Shin Kim
    • , Roberto Lozano
    •  & Soon-Chun Jeong
  • Article
    | Open Access

    It has been reported that several phytohormones are involved in the regulation of grain weight, but the role of jasmonic acids (JA) remains elusive. Here, via bulked segregant analysis (BSA)-based cloning, the authors show keto-acyl thiolase 2B involved in β-oxidation during JA synthesis is a positive regulator of wheat grain weight.

    • Yun Chen
    • , Yan Yan
    •  & Jin-Ying Gou
  • Article
    | Open Access

    Fruit firmness is an important target for breeders and a key determinant of shelf life for many fruits. Here the authors show that mutating tomato FIS1, a GA2-oxidase, increases the concentration of bioactive gibberellins, enhances cutin and wax biosynthesis and increases fruit firmness.

    • Ren Li
    • , Shuai Sun
    •  & Xia Cui
  • Article
    | Open Access

    The putative causal agent of citrus greening Candidatus Liberibacter asiaticus (CLas) cannot be cultured, which hampers finding new therapies to control this devastating disease. Here, the authors show that hairy roots support CLas propagation and enable high throughput antimicrobial screening.

    • Sonia Irigoyen
    • , Manikandan Ramasamy
    •  & Kranthi K. Mandadi
  • Article
    | Open Access

    Understanding the mechanism of high-temperature tolerance will help to breed crops adaptive to warming climate. Here, the authors show SLG1, a cytosolic tRNA 2-thiolation protein 2 encoding gene, is differentiated between the two Asian cultivated rice subspecies and confers high temperature tolerance of indica rice.

    • Yufang Xu
    • , Li Zhang
    •  & Shanguo Yao
  • Article
    | Open Access

    The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.

    • Therese Mitros
    • , Adam M. Session
    •  & Daniel S. Rokhsar
  • Article
    | Open Access

    Very little is known about how vitreous endosperm in the mature maize kernel is created. Here, via map-based cloning, the authors find that mutation of a β-carotene hydroxylase 3 encoding gene Ven1 affects carotenoids and lipids composition, which consequently influences amyloplast envelope integrity.

    • Haihai Wang
    • , Yongcai Huang
    •  & Yongrui Wu
  • Article
    | Open Access

    The meiotic transmissibility and progeny phenotypic influence of graft-mediated epigenetic changes remain unclear. Here, the authors use the msh1 mutant in the rootstock to trigger heritable enhanced growth vigor in Arabidopsis and tomato, and show it is associated with the RNA-directed DNA methylation pathway.

    • Hardik Kundariya
    • , Xiaodong Yang
    •  & Sally A. Mackenzie
  • Article
    | Open Access

    Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.

    • Fu-Sheng Yang
    • , Shuai Nie
    •  & Jian-Feng Mao
  • Perspective
    | Open Access

    Biofortification is an effective means to reduce micronutrient malnutrition. Here, the authors review recent advances in biofortification and propose stacking multiple micronutrient traits into high-yielding varieties through the combination of conventional breeding and genetic engineering approaches.

    • Dominique Van Der Straeten
    • , Navreet K. Bhullar
    •  & Howarth Bouis
  • Article
    | Open Access

    The molecular connection between nitrogen utilization efficiency (NUE) and biomass production is unclear. Here, the authors show that differences in NUE and cellulose biogenesis between rice indica and japonica subspecies can be explained by variation at the MYB61 locus, which is regulated by the NUE regulator GRF4.

    • Yihong Gao
    • , Zuopeng Xu
    •  & Yihua Zhou
  • Article
    | Open Access

    This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.

    • Alicia C. Bertolotti
    • , Ryan M. Layer
    •  & Daniel J. Macqueen
  • Article
    | Open Access

    Grasses have diverse inflorescence morphologies, but the underlying genetic mechanisms are unclear. Here, the authors report a TCP transcription factor COM1 affects cell growth through regulation of cell wall properties and promotes branch formation in non-Triticeae grasses but branch inhibition in barley (Triticeae).

    • Naser Poursarebani
    • , Corinna Trautewig
    •  & Thorsten Schnurbusch
  • Article
    | Open Access

    Mechanism of high altitude adaptation of wheat remains unknown. Here, the authors assemble the draft genome of a Tibetan semi-wild wheat accession and resequence 245 wheat accessions to reveal that Tibetan semi-wild wheat has been de-domesticated from local landraces to adapt to high altitude.

    • Weilong Guo
    • , Mingming Xin
    •  & Qixin Sun
  • Article
    | Open Access

    Predicting crop performance in environments with limited field testing is challenging. Here the authors combine field experimental, DNA sequence, and weather data to predict genotypes’ future performance. They demonstrate the potential of this approach on a large dataset of wheat grain yield.

    • Gustavo de los Campos
    • , Paulino Pérez-Rodríguez
    •  & José Crossa
  • Article
    | Open Access

    Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

    • Michael Abrouk
    • , Hanin Ibrahim Ahmed
    •  & Simon G. Krattinger
  • Article
    | Open Access

    Tea is an important beverage crop with a large and heterozygous genome. Here, the authors assemble the genome of the cultivar Longjing 43 and conduct a population genetics study to reveal divergent selection for disease resistance and flavor between the two variety groups.

    • Xinchao Wang
    • , Hu Feng
    •  & Yajun Yang
  • Article
    | Open Access

    Transposable element insertion polymorphisms (TIPs) are a potential source of large effect alleles. Here, the authors use genome resequencing data for 602 tomato accessions together with transcriptomic and extensive phenotypic information to investigate the contribution of TIPs to tomato diversity.

    • Marisol Domínguez
    • , Elise Dugas
    •  & Leandro Quadrana
  • Article
    | Open Access

    Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.

    • Weiyi Zhang
    • , Youjun Zhang
    •  & Weiwei Wen
  • Article
    | Open Access

    Grapevine is one of a few ancestrally dioecious crops that are reverted to hermaphroditism during domestication. Here, the authors identify candidate genes related to male- and female-sterility in grapes and describe the genetic process that led to hermaphroditism during domestication.

    • Mélanie Massonnet
    • , Noé Cochetel
    •  & Dario Cantu