Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy.

Abstract:

:Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either 'Landraces' or 'Wild and Weedy' genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.

journal_name

Plant Biotechnol J

authors

Campbell BC,Gilding EK,Mace ES,Tai S,Tao Y,Prentis PJ,Thomelin P,Jordan DR,Godwin ID

doi

10.1111/pbi.12578

subject

Has Abstract

pub_date

2016-12-01 00:00:00

pages

2240-2253

issue

12

eissn

1467-7644

issn

1467-7652

journal_volume

14

pub_type

杂志文章
  • A maize phytochrome-interacting factors protein ZmPIF1 enhances drought tolerance by inducing stomatal closure and improves grain yield in Oryza sativa.

    abstract::Phytochrome-interacting factors (PIFs) play major roles in regulating plant growth and development, but their roles in drought stress remain elusive. Here, we cloned and characterized a maize (Zea mays) PIF transcription factor, ZmPIF1. The expression level of ZmPIF1 was significantly induced by independent drought an...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12878

    authors: Gao Y,Wu M,Zhang M,Jiang W,Ren X,Liang E,Zhang D,Zhang C,Xiao N,Li Y,Dai Y,Chen J

    更新日期:2018-07-01 00:00:00

  • Bt rice could provide ecological resistance against nontarget planthoppers.

    abstract::Genetically engineered (GE) rice lines expressing Lepidoptera-active insecticidal cry genes from the bacterium Bacillus thuringiensis (Bt) have been developed in China. Field surveys indicated that Bt rice harbours fewer rice planthoppers than non-Bt rice although planthoppers are not sensitive to the produced Bt Cry ...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12911

    authors: Wang X,Liu Q,Meissle M,Peng Y,Wu K,Romeis J,Li Y

    更新日期:2018-10-01 00:00:00

  • RNAi trigger fragment truncation attenuates soybean FAD2-1 transcript suppression and yields intermediate oil phenotypes.

    abstract::Suppression of the microsomal ω6 oleate desaturase during the seed development of soybean (Glycine max) with the 420-bp soybean FAD2-1A intron as RNAi trigger shifts the conventional fatty acid composition of soybean oil from 20% oleic and 60% polyunsaturates to one containing greater than 80% oleic acid and less than...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2010.00573.x

    authors: Wagner N,Mroczka A,Roberts PD,Schreckengost W,Voelker T

    更新日期:2011-09-01 00:00:00

  • Light-dependent regulation of ascorbate in tomato by a monodehydroascorbate reductase localized in peroxisomes and the cytosol.

    abstract::Ascorbate is a powerful antioxidant in plants, and its levels are an important quality criteria in commercial species. Factors influencing these levels include environmental variations, particularly light, and the genetic control of its biosynthesis, recycling and degradation. One of the genes involved in the recyclin...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12020

    authors: Gest N,Garchery C,Gautier H,Jiménez A,Stevens R

    更新日期:2013-04-01 00:00:00

  • Enhancing C3 photosynthesis: an outlook on feasible interventions for crop improvement.

    abstract::Despite the declarations and collective measures taken to eradicate hunger at World Food Summits, food security remains one of the biggest issues that we are faced with. The current scenario could worsen due to the alarming increase in world population, further compounded by adverse climatic conditions, such as increa...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12246

    authors: Singh J,Pandey P,James D,Chandrasekhar K,Achary VM,Kaul T,Tripathy BC,Reddy MK

    更新日期:2014-12-01 00:00:00

  • A new dominant Arabidopsis transparent testa mutant, sk21-D, and modulation of seed flavonoid biosynthesis by KAN4.

    abstract::Flavonoids are widely distributed in plants and play important roles in human and animal health and nutrition. Model plants with discernible flavonoid phenotypes, such as Arabidopsis seed patterning lines, are valuable tools that can provide avenues for understanding flavonoid and proanthocyanidin accumulation pattern...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2010.00525.x

    authors: Gao P,Li X,Cui D,Wu L,Parkin I,Gruber MY

    更新日期:2010-12-01 00:00:00

  • Production of cecropin A in transgenic rice plants has an impact on host gene expression.

    abstract::Expression of the cecropin A gene in rice confers resistance to the rice blast fungus Magnaporthe oryzae. In this study, a polymerase chain reaction-based suppression subtractive hybridization approach was used to generate a cDNA macroarray from the elite japonica rice (Oryza sativa L.) cultivar 'Senia'. Gene expressi...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2008.00339.x

    authors: Campo S,Manrique S,García-Martínez J,San Segundo B

    更新日期:2008-08-01 00:00:00

  • Suppression of α-amylase genes improves quality of rice grain ripened under high temperature.

    abstract::High temperature impairs rice (Oryza sativa) grain filling by inhibiting the deposition of storage materials such as starch, resulting in mature grains with a chalky appearance, currently a major problem for rice farming in Asian countries. Such deterioration of grain quality is accompanied by the altered expression o...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2012.00741.x

    authors: Hakata M,Kuroda M,Miyashita T,Yamaguchi T,Kojima M,Sakakibara H,Mitsui T,Yamakawa H

    更新日期:2012-12-01 00:00:00

  • Stable expression of silencing-suppressor protein enhances the performance and longevity of an engineered metabolic pathway.

    abstract::Transgenic engineering of plants is important in both basic and applied research. However, the expression of a transgene can dwindle over time as the plant's small (s)RNA-guided silencing pathways shut it down. The silencing pathways have evolved as antiviral defence mechanisms, and viruses have co-evolved viral silen...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12506

    authors: Naim F,Shrestha P,Singh SP,Waterhouse PM,Wood CC

    更新日期:2016-06-01 00:00:00

  • MicroRNA156 as a promising tool for alfalfa improvement.

    abstract::A precursor of miR156 (MsmiR156d) was cloned and overexpressed in alfalfa (Medicago sativa L.) as a means to enhance alfalfa biomass yield. Of the five predicted SPL genes encoded by the alfalfa genome, three (SPL6, SPL12 and SPL13) contain miR156 cleavage sites and their expression was down-regulated in transgenic al...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12308

    authors: Aung B,Gruber MY,Amyot L,Omari K,Bertrand A,Hannoufa A

    更新日期:2015-08-01 00:00:00

  • The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions.

    abstract::Drought conditions limit agricultural production by preventing crops from reaching their genetically predetermined maximum yields. Here, we present the results of field evaluations of rice overexpressing OsNAC9, a member of the rice NAC domain family. Root-specific (RCc3) and constitutive (GOS2) promoters were used to...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2012.00697.x

    authors: Redillas MC,Jeong JS,Kim YS,Jung H,Bang SW,Choi YD,Ha SH,Reuzeau C,Kim JK

    更新日期:2012-09-01 00:00:00

  • Engineering linear, branched-chain triterpene metabolism in monocots.

    abstract::Triterpenes are thirty-carbon compounds derived from the universal five-carbon prenyl precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Normally, triterpenes are synthesized via the mevalonate (MVA) pathway operating in the cytoplasm of eukaryotes where DMAPP is condensed with two IPPs to...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12983

    authors: Kempinski C,Jiang Z,Zinck G,Sato SJ,Ge Z,Clemente TE,Chappell J

    更新日期:2019-02-01 00:00:00

  • Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae.

    abstract::The plant pathogen, Pseudomonas syringae (Ps), together with related Ps species, infects and attacks a wide range of agronomically important crops, including tomato, kiwifruit, pepper, olive and soybean, causing economic losses. Currently, chemicals and introduced resistance genes are used to protect plants against th...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13294

    authors: Rooney WM,Grinter RW,Correia A,Parkhill J,Walker DC,Milner JJ

    更新日期:2020-05-01 00:00:00

  • Up-regulation of an N-terminal truncated 3-hydroxy-3-methylglutaryl CoA reductase enhances production of essential oils and sterols in transgenic Lavandula latifolia.

    abstract::Spike lavender (Lavandula latifolia) essential oil is widely used in the perfume, cosmetic, flavouring and pharmaceutical industries. Thus, modifications of yield and composition of this essential oil by genetic engineering should have important scientific and commercial applications. We generated transgenic spike lav...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2007.00286.x

    authors: Muñoz-Bertomeu J,Sales E,Ros R,Arrillaga I,Segura J

    更新日期:2007-11-01 00:00:00

  • Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides.

    abstract::Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and u...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12473

    authors: Rivera-Torres N,Kmiec EB

    更新日期:2016-02-01 00:00:00

  • Oral immunotherapy with transgenic rice seed containing destructed Japanese cedar pollen allergens, Cry j 1 and Cry j 2, against Japanese cedar pollinosis.

    abstract::Transgenic rice accumulating the modified major Japanese cedar pollen allergens, Cryptomeria japonica 1 (Cry j 1) and Cryptomeria japonica 2 (Cry j 2), which were deconstructed by fragmentation and shuffling, respectively, in the edible part of the seed was generated by transformation of a good-tasting rice variety, '...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12007

    authors: Wakasa Y,Takagi H,Hirose S,Yang L,Saeki M,Nishimura T,Kaminuma O,Hiroi T,Takaiwa F

    更新日期:2013-01-01 00:00:00

  • BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

    abstract::The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12513

    authors: Staňková H,Hastie AR,Chan S,Vrána J,Tulpová Z,Kubaláková M,Visendi P,Hayashi S,Luo M,Batley J,Edwards D,Doležel J,Šimková H

    更新日期:2016-07-01 00:00:00

  • Mice fed on a diet enriched with genetically engineered multivitamin corn show no sub-acute toxic effects and no sub-chronic toxicity.

    abstract::Multivitamin corn is a novel genetically engineered variety that simultaneously produces high levels of β-carotene, ascorbate and folate, and therefore has the potential to address simultaneously multiple micronutrient deficiencies caused by the lack of vitamins A, B9 and C in developing country populations. As part o...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2012.00730.x

    authors: Arjó G,Capell T,Matias-Guiu X,Zhu C,Christou P,Piñol C

    更新日期:2012-12-01 00:00:00

  • Control limits for accumulation of plant metabolites: brute force is no substitute for understanding.

    abstract::Which factors limit metabolite accumulation in plant cells? Are theories on flux control effective at explaining the results? Many biotechnologists cling to the idea that every pathway has a rate limiting enzyme and target such enzymes first in order to modulate fluxes. This often translates into large effects on meta...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12035

    authors: Morandini P

    更新日期:2013-02-01 00:00:00

  • Chloroplast-derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars.

    abstract::It is widely recognized that biofuel production from lignocellulosic materials is limited by inadequate technology to efficiently and economically release fermentable sugars from the complex multi-polymeric raw materials. Therefore, endoglucanases, exoglucanase, pectate lyases, cutinase, swollenin, xylanase, acetyl xy...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2009.00486.x

    authors: Verma D,Kanagaraj A,Jin S,Singh ND,Kolattukudy PE,Daniell H

    更新日期:2010-04-01 00:00:00

  • A pathogenesis-related protein GmPR08-Bet VI promotes a molecular interaction between the GmSHMT08 and GmSNAP18 in resistance to Heterodera glycines.

    abstract::Soybean cyst nematode (SCN, Heterodera glycines) is the most devastating pest affecting soybean production worldwide. SCN resistance requires both the GmSHMT08 and the GmSNAP18 in 'Peking'-type resistance. Here, we describe the molecular interaction between GmSHMT08 and GmSNAP18, which is potentiated by a pathogenesis...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13343

    authors: Lakhssassi N,Piya S,Bekal S,Liu S,Zhou Z,Bergounioux C,Miao L,Meksem J,Lakhssassi A,Jones K,Kassem MA,Benhamed M,Bendahmane A,Lambert K,Boualem A,Hewezi T,Meksem K

    更新日期:2020-08-01 00:00:00

  • Immunogenicity of plant-produced porcine circovirus-like particles in mice.

    abstract::Porcine circovirus type 2 (PCV-2) is the main causative agent associated with a group of diseases collectively known as porcine circovirus-associated disease (PCAD). There is a significant economic strain on the global swine industry due to PCAD and the production of commercial PCV-2 vaccines is expensive. Plant expre...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13097

    authors: Gunter CJ,Regnard GL,Rybicki EP,Hitzeroth II

    更新日期:2019-09-01 00:00:00

  • Foreign gene products can be enhanced by introduction into low storage protein mutants.

    abstract::Transgenic rice expressing soybean glycinin in its endosperm was crossed with two types of low-glutelin mutants to determine how much storage the protein mutants can contribute to increases in glycinin accumulation. The glycinin level (102 microg/100 mg seed) in the parental transgenic line was enhanced to approximate...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1046/j.1467-7652.2003.00038.x

    authors: Tada Y,Utsumi S,Takaiwa F

    更新日期:2003-11-01 00:00:00

  • Commercialization of new biotechnology: a systematic review of 16 commercial case studies in a novel manufacturing sector.

    abstract::The 1980s and 1990s saw a major expansion of biotechnology into new areas of science including genomics and recombinant technologies. This was coupled to the widespread emergence of academics into the commercial sector as they were encouraged to spin out companies or commercialize their intellectual property. There we...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12426

    authors: Paul MJ,Thangaraj H,Ma JK

    更新日期:2015-10-01 00:00:00

  • Transient expression assays in grapevine: a step towards genetic improvement.

    abstract::In the past few years, the usefulness of transient expression assays has continuously increased for the characterization of unknown gene function and metabolic pathways. In grapevine (Vitis vinifera L.), one of the most economically important fruit crops in the world, recent systematic sequencing projects produced man...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12294

    authors: Jelly NS,Valat L,Walter B,Maillot P

    更新日期:2014-12-01 00:00:00

  • Recombinant aryl hydrocarbon receptors for bioassay of aryl hydrocarbon receptor ligands in transgenic tobacco plants.

    abstract::Dioxin residues widely contaminate soil and agricultural products at low concentrations and may accumulate in organisms at the top of food chains owing to their physicochemical properties. In this study, we have developed novel, dioxin-inducible, reporter gene expression systems regulated by recombinant aryl hydrocarb...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2008.00378.x

    authors: Kodama S,Okada K,Akimoto K,Inui H,Ohkawa H

    更新日期:2009-02-01 00:00:00

  • Enhancing the expression of starch synthase class IV results in increased levels of both transitory and long-term storage starch.

    abstract::Starch is an important renewable raw material with an increasing number of applications. Several attempts have been made to obtain plants that produce modified versions of starch or higher starch yield. Most of the approaches designed to increase the levels of starch have focused on the increment of the amount of ADP-...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2011.00626.x

    authors: Gámez-Arjona FM,Li J,Raynaud S,Baroja-Fernández E,Muñoz FJ,Ovecka M,Ragel P,Bahaji A,Pozueta-Romero J,Mérida Á

    更新日期:2011-12-01 00:00:00

  • High-amylose rice improves indices of animal health in normal and diabetic rats.

    abstract::A high-amylose rice with 64.8% amylose content (AC) was developed by transgenic inhibition of two isoforms of starch branching enzyme (SBE), SBEI and SBEIIb, in an indica rice cultivar. The expression of SBEI and SBEIIb was completely inhibited in the transgenic line, whereas the expression of granule-bound starch syn...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2011.00667.x

    authors: Zhu L,Gu M,Meng X,Cheung SC,Yu H,Huang J,Sun Y,Shi Y,Liu Q

    更新日期:2012-04-01 00:00:00

  • Coupling two mercury resistance genes in Eastern cottonwood enhances the processing of organomercury.

    abstract::Eastern cottonwood (Populus deltoides Bartr. ex Marsh.) trees were engineered to express merA (mercuric ion reductase) and merB (organomercury lyase) transgenes in order to be used for the phytoremediation of mercury-contaminated soils. Earlier studies with Arabidopsis thaliana and Nicotiana tabacum showed that this g...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2006.00236.x

    authors: Lyyra S,Meagher RB,Kim T,Heaton A,Montello P,Balish RS,Merkle SA

    更新日期:2007-03-01 00:00:00

  • Overexpression of serine acetyltransferase in maize leaves increases seed-specific methionine-rich zeins.

    abstract::Maize kernels do not contain enough of the essential sulphur-amino acid methionine (Met) to serve as a complete diet for animals, even though maize has the genetic capacity to store Met in kernels. Prior studies indicated that the availability of the sulphur (S)-amino acids may limit their incorporation into seed stor...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12851

    authors: Xiang X,Wu Y,Planta J,Messing J,Leustek T

    更新日期:2018-05-01 00:00:00