Integrated mapping and characterization of the gene underlying the okra leaf trait in Gossypium hirsutum L

Shaping leaves through TALE homeodomain transcription factors

The first TALE homeodomain transcription factor gene to be described in plants was maize knotted1 (kn1). Dominant mutations in kn1 disrupt leaf development, with abnormal knots of tissue forming in the leaf blade. kn1 was found to be expressed in the shoot meristem but not in a peripheral region that gives rise to leaves. Furthermore, KN1 and closely related proteins were excluded from initiating and developing leaves. These findings were a prelude to a large body of work wherein TALE homeodomain proteins have been identified as vital regulators of meristem homeostasis and organ development in plants. KN1 homologues are widely represented across land plant taxa. Thus, studying the regulation and mechanistic action of this gene class has allowed investigations into the evolution of diverse plant morphologies. This review will focus on the function of TALE homeodomain transcription factors in leaf development in eudicots. Here, we discuss how TALE homeodomain proteins contribute to a spectrum of leaf forms, from the simple leaves of Arabidopsis thaliana to the compound leaves of Cardamine hirsuta and species beyond the Brassicaceae.

Dissecting the major genetic components underlying cotton lint development

Numerous genetic loci and several functionally characterized genes have been linked to determination of lint percentage (lint%), one of the most important cotton yield components, but we still know little about the major genetic components underlying lint%. Here, we first linked the genetic loci containing MYB25-like_At and HD1_At to the fiberless seed trait of 'SL1-7-1' and found that MYB25-like_At and HD1_At were very lowly expressed in 'SL1-7-1' ovules during fiber initiation. We then dissected the genetic components involved in determination of lint% using segregating populations derived from crosses of fuzzless mutants and intermediate segregants with different lint%, which not only confirmed the HD1_At locus but identified the HD1_Dt locus as being the major genetic components contributing to fiber initiation and lint%. The segregating populations also allowed us to evaluate the relative contributions of MYB25-like_At, MYB25-like_Dt, HD1_At, and HD1_Dt to lint%. Haplotype analysis of an Upland cotton (Gossypium hirsutum) population with 723 accessions (including 81 fuzzless seed accessions) showed that lint% of the accessions with the LP allele (higher lint%) at MYB25-like_At, MYB25-like_Dt, or HD1_At was significantly higher than that with the lp allele (lower lint%). The lint% of the Upland cotton accessions with 3 or 4 LP alleles at MYB25-like and HD1 was significantly higher than that with 2 LP alleles. The results prompted us to propose a strategy for breeding high-yielding cotton varieties, i.e. pyramiding the LP alleles of MYB25-like and HD1 with new lint% LP alleles without negative impact on seed size and fiber quality.

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

Inheritance of dwarfism and narrow lobed-leaf in two rapeseed (Brassica napus L.) mutant lines

There is a need for dwarf and narrow lobed-leaves rapeseed cultivars to reduce transpiration under drought prone areas. A dwarf mutant line 'H2M-1' and a mutant with reduced lobed-leaf 'H2M-2' were developed. To exploit these mutated traits properly in an effective breeding program, one should understand their mode of inheritance. There are conflicting findings for plant dwarfism and limited studies for leaf size in mutant genetic backgrounds. Therefore, the objective of this study was to investigate the inheritance of dwarfism and narrow lobed-leaf mutated traits. Plants of the wild-type variety 'INRA-CZH2' were reciprocally crossed with plants of the line 'H2M-1' and plants of the line 'H2M-2'. A genetic study was conducted by analyzing segregation of mutated traits in F₁, F₂ and BC₁F₁ generations. The results revealed that two recessive genes with dominant epistasis action controlled the heredity of plant height in the dwarf line, whereas only a single recessive gene is involved in determining reduced lobed-leaf in the line H2M-2. Thus, there is a possibility to easily and quickly transfer these characters into rapeseed breeding germplasm or varieties towards the development of suitable cultivars for areas marked by increasing drought stress.

Genomic prediction of cotton fibre quality and yield traits using Bayesian regression methods

Genomic selection or genomic prediction (GP) has increasingly become an important molecular breeding technology for crop improvement. GP aims to utilise genome-wide marker data to predict genomic breeding value for traits of economic importance. Though GP studies have been widely conducted in various crop species such as wheat and maize, its application in cotton, an essential renewable textile fibre crop, is still significantly underdeveloped. We aim to develop a new GP-based breeding system that can improve the efficiency of our cotton breeding program. This article presents a GP study on cotton fibre quality and yield traits using 1385 breeding lines from the Commonwealth Scientific and Industrial Research Organisation (CSIRO, Australia) cotton breeding program which were genotyped using a high-density SNP chip that generated 12,296 informative SNPs. The aim of this study was twofold: (1) to identify the models and data sources (i.e. genomic and pedigree) that produce the highest prediction accuracies; and (2) to assess the effectiveness of GP as a selection tool in the CSIRO cotton breeding program. The prediction analyses were conducted under various scenarios using different Bayesian predictive models. Results highlighted that the model combining genomic and pedigree information resulted in the best cross validated prediction accuracies: 0.76 for fibre length, 0.65 for fibre strength, and 0.64 for lint yield. Overall, this work represents the largest scale genomic selection studies based on cotton breeding trial data. Prediction accuracies reported in our study indicate the potential of GP as a breeding tool for cotton. The study highlighted the importance of incorporating pedigree and environmental factors in GP models to optimise the prediction performance.

Cotton Breeding in Australia: Meeting the Challenges of the 21st Century

The Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program is the sole breeding effort for cotton in Australia, developing high performing cultivars for the local industry which is worth∼AU$3 billion per annum. The program is supported by Cotton Breeding Australia, a Joint Venture between CSIRO and the program's commercial partner, Cotton Seed Distributors Ltd. (CSD). While the Australian industry is the focus, CSIRO cultivars have global impact in North America, South America, and Europe. The program is unique compared with many other public and commercial breeding programs because it focuses on diverse and integrated research with commercial outcomes. It represents the full research pipeline, supporting extensive long-term fundamental molecular research; native and genetically modified (GM) trait development; germplasm enhancement focused on yield and fiber quality improvements; integration of third-party GM traits; all culminating in the release of new commercial cultivars. This review presents evidence of past breeding successes and outlines current breeding efforts, in the areas of yield and fiber quality improvement, as well as the development of germplasm that is resistant to pests, diseases and abiotic stressors. The success of the program is based on the development of superior germplasm largely through field phenotyping, together with strong commercial partnerships with CSD and Bayer CropScience. These relationships assist in having a shared focus and ensuring commercial impact is maintained, while also providing access to markets, traits, and technology. The historical successes, current foci and future requirements of the CSIRO cotton breeding program have been used to develop a framework designed to augment our breeding system for the future. This will focus on utilizing emerging technologies from the genome to phenome, as well as a panomics approach with data management and integration to develop, test and incorporate new technologies into a breeding program. In addition to streamlining the breeding pipeline for increased genetic gain, this technology will increase the speed of trait and marker identification for use in genome editing, genomic selection and molecular assisted breeding, ultimately producing novel germplasm that will meet the coming challenges of the 21st Century.

Overexpression of BnaAGL11, a MADS-Box Transcription Factor, Regulates Leaf Morphogenesis and Senescence in Brassica napus

Previous studies have reported that SEEDSTICK/AGAMOUS-LIKE 11 (AtSTK/AtAGL11), a MADS-box transcription factor, plays important roles in many biological processes in Arabidopsis thaliana. However, the function of BnaAGL11, an AtAGL11 homologous gene from Brassica napus, in leaf development remains unknown. Here, we found that the ectopic expression of any copy of Bna.C09.AGL11, Bna.A03.AGL11, and Bna.A09.AGL11 in A. thaliana led to smaller and curly leaves and promoted leaf senescence. Consistently, the overexpression of Bna.C09.AGL11 in B. napus also caused smaller and curly leaves and accelerated leaf senescence. Furthermore, we demonstrated that Bna.C09.AGL11 controlled leaf morphogenesis by indirectly downregulating the genes of Bna.A01.DWF4 and Bna.C07.PGX3 and promoted leaf senescence by indirectly upregulating the genes of Bna.A04.ABI5, Bna.A05.ABI5, Bna.C04.ABI5-1, and Bna.C01.SEN4 and directly activating the transcription of Bna.C04.ABI5-2 and Bna.C03.SEN4 genes. Our results provide new insights into the underlying regulatory mechanism of BnaAGL11 during leaf development in B. napus.

Map-based cloning and promoter variation analysis of the lobed leaf gene BoLMI1a in ornamental kale (Brassica oleracea L. var. acephala)

BACKGROUND

Leaf shape is an important agronomic trait in ornamental kale (Brassica oleracea L. var. acephala). Although some leaf shape-related genes have been reported in ornamental kale, the detailed mechanism underlying leaf shape formation is still unclear. Here, we report a lobed-leaf trait in ornamental kale, aiming to analyze its inheritance and identify the strong candidate gene.

RESULTS

Genetic analysis of F₂ and BC₁ populations demonstrate that the lobed-leaf trait in ornamental kale is controlled by a single dominant gene, termed BoLl-1 (Brassica oleracea lobed-leaf). By performing whole-genome resequencing and linkage analyses, the BoLl-1 gene was finely mapped to a 127-kb interval on chromosome C09 flanked by SNP markers SL4 and SL6, with genetic distances of 0.6 cM and 0.6 cM, respectively. Based on annotations of the genes within this interval, Bo9g181710, an orthologous gene of LATE MERISTEM IDENTITY 1 (LMI1) in Arabidopsis, was predicted as the candidate for BoLl-1, and was renamed BoLMI1a. The expression level of BoLMI1a in lobed-leaf parent 18Q2513 was significantly higher compared with unlobed-leaf parent 18Q2515. Sequence analysis of the parental alleles revealed no sequence variations in the coding sequence of BoLMI1a, whereas a 1737-bp deletion, a 92-bp insertion and an SNP were identified within the BoLMI1a promoter region of parent 18Q2513. Verification analyses with BoLMI1a-specific markers corresponding to the promoter variations revealed that the variations were present only in the lobed-leaf ornamental kale inbred lines.

CONCLUSIONS

This study identified a lobed-leaf gene BoLMI1a, which was fine-mapped to a 127-kb fragment. Three variations were identified in the promoter region of BoLMI1a. The transcription level of BoLMI1a between the two parents exhibited great difference, providing new insight into the molecular mechanism underlying leaf shape formation in ornamental kale.

Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0-6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

Fine Mapping of a Locus Underlying the Ectopic Blade-Like Outgrowths on Leaf and Screening Its Candidate Genes in Rapeseed (Brassica napus L.)

Leaf is an important organ for higher plants, and the shape of it is one of the crucial traits of crops. In this study, we investigated a unique aberrant leaf morphology trait in a mutational rapeseed material, which displayed ectopic blade-like outgrowths on the adaxial side of leaf. The abnormal line 132000B-3 was crossed with the normal line 827-3. Based on the F_{2 : 3} family, we constructed two DNA pools (normal pool and abnormal pool) by the bulked segregant analysis (BSA) method and performed whole genome re-sequencing (WGR), obtaining the single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) data. The SNP-index method was used to calculate the Δ(SNP/InDel-index), and then an association region was identified on chromosome A10 with a length of 5.5 Mbp, harboring 1048 genes totally. Subsequently, the fine mapping was conducted by using the penta-primer amplification refractory mutation system (PARMS), and the associated region was narrowed down to a 35.1-kbp segment, containing only seven genes. These seven genes were then analyzed according to their annotations and finally, BnA10g0422620 and BnA10g0422610, orthologs of LATE MERISTEM IDENTITY1 (LMI1) gene from Arabidopsis and REDUCED COMPLEXITY (RCO) gene from its relative Cardamine hirsuta, respectively, were identified as the candidate genes responding to this blade-like outgrowth trait in rapeseed. This study provides a novel perspective into the leaf formation in Brassica plants.

Productivity and quality of horticultural crops through co-inoculation of arbuscular mycorrhizal fungi and plant growth promoting bacteria

Associations between plants and microorganisms exist in nature, and they can either be beneficial or detrimental to host plants. Promoting beneficial plant-microbe interaction for increased crop yield and quality is one pathway to eco-friendly and sustainable crop production. Arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPB) are microorganisms that are beneficial to horticultural crops. Arbuscular mycorrhizal fungi establish symbioses with plant roots which help to improve nutrient uptake by the host plant and alter its physiology to withstand external abiotic factors and pathogens. Plant growth promoting bacteria promote plant growth either directly by aiding resource acquisition and controlling the levels of plant hormones or indirectly by reducing the inhibitory effects of phytopathogens. Co-inoculation of both organisms combines the benefits of each for increased crop productivity. Even though the co-inoculation of PGPB and AMF have been shown to enhance the yield and quality of crops, its benefits have fully not been exploited for horticultural crops. In this review, the response of horticultural crops to co-inoculation with PGPB and AMF with particular interest to the impact on the yield and crop quality was discussed. We explained some of the mechanisms responsible for the synergy between AMF and PGPB in plant growth promotion. Finally, suggestions on areas that need to be researched further to exploit and improve the effects of these organisms were highlighted.

Ecotoxicological Assessment of a Glyphosate-Based Herbicide in Cover Plants: Medicago sativa L. as a Model Species

Despite the several innovations that have been incorporated in agriculture, the use of herbicides, especially glyphosate (GLY), is still the major tool for weed control. Although this herbicide has a notable worldwide representation, concerns about its environmental safety were recently raised, with a lot of divergence between studies on its non-target toxicity. Therefore, it is of utmost importance to understand the risks of this herbicide to non-target plants, including cover crop species, which have a crucial role in maintaining agroecosystems functions and in preventing soil erosion. Thus, this work aims to evaluate the growth and physiological responses of a cover plant species (Medicago sativa L.) exposed to increasing concentrations of a GLY-based herbicide (GBH), particularly focusing on the oxidative metabolism. The growth of roots and shoots was affected, being this effect accompanied by a rise of lipid peroxidation, suggesting the occurrence of oxidative stress, and by an activation of the antioxidant (AOX) system. Indeed, the results showed that adverse effects are visible at active ingredient concentrations of 8.0 mg kg−1, with the lowest EC50 being 12 mg kg−1, showing that GBH-contaminated soils may pose a risk to the survival of non-target plants in the most contaminated areas. Overall, these findings proved that GBH greatly impairs the growth of a non-target plant, strengthening the need of additional studies to unravel the real risks associated with the over usage of this pesticide, since there is an evident lack of studies performed with contaminated soils.

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

Background

The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization.

Results

In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC).

Conclusions

This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

Genetic Identification and Transcriptome Analysis of Lintless and Fuzzless Traits in Gossypium arboreum L

Cotton fibres, as single cells arising from the seed coat, can be classified as lint and fuzz according to their final length. Gossypium arboreum is a cultivated diploid cotton species and a potential donor of the A subgenome of the more widely grown tetraploid cottons. In this study, we performed genetic studies on one lintless and seven fuzzless G. arboreum accessions. Through association and genetic linkage analyses, a recessive locus on Chr06 containing GaHD-1 was found to be the likely gene underlying the lintless trait. GaHD-1 carried a mutation at a splicing acceptor site that resulted in alternative splicing and a deletion of 247 amino acid from the protein. The regions containing GaGIR1 and GaMYB25-like were found to be associated with fuzz development in G. arboreum, with the former being the major contributor. Comparative transcriptome analyses using 0-5 days post-anthesis (dpa) ovules from lintless, fuzzless, and normal fuzzy seed G. arboreum accessions revealed gene modules and hub genes potentially important for lint and fuzz initiation and development. Three significant modules and 26 hub genes associated with lint fibre initiation were detected by weighted gene co-expression network analysis. Similar analyses identified three vital modules and 10 hub genes to be associated with fuzz development. The findings in this study contribute to understanding the complex molecular mechanism(s) regulating fibre initiation and development and indicate that G. arboreum may have fibre developmental pathways different from tetraploid cotton. It also provides candidate genes for further investigation into modifying fibre development in G. arboreum.

LMI1-like and KNOX1 genes coordinately regulate plant leaf development in dicotyledons

This report reveals that the LMI1-like and KNOX1 genes coordinately control the leaf development and different combinations of those genes which produce diverse leaf shapes including broad, lobed and compound leaves. Class I KNOTTED1-like homeobox (KNOX1) genes are involved in compound leaf development and are repressed by the ASYMMETRIC LEAVES1 (AS1)-AS2 complex. Cotton plants have a variety of leaf shapes, including broad leaves and lobed leaves. GhOKRA, a LATE MERISTEM IDENTITY 1 (LMI1)-like gene, controls the development of an okra leaf shape. We cloned the corresponding cotton homologs of Arabidopsis thaliana AS1 and AS2 and seven KNOX1 genes. Through virus-induced gene silencing technology, we found that either GhAS1 or GhAS2-silenced cotton plants showed a great change in leaf shape from okra leaves to trifoliolate dissected leaves. In the shoot tips of these plants, the expression of the cotton ortholog of Knotted in A. thaliana 1 (KNAT1), GhKNOTTED1-LIKE2/3/4 (GhKNL2/3/4), was increased. However, GhKNOX1s-silenced plants maintained the wild-type okra leaves. A novel dissected-like leaf in A. thaliana was further generated by crossing plants constitutively expressing GhOKRA with either as1-101 or as2-101 mutant plants. The dissected-like leaves showed two different leaf vein patterns. This report reveals that the LMI1-like and KNOX1 genes coordinately control leaf development, and different combinations of these genes produce diverse leaf shapes including broad leaves, lobed leaves and compound leaves. This is the first report on the artificial generation of compound leaves from simple leaves in cotton.

Promoter variations in a homeobox gene, BnA10.LMI1, determine lobed leaves in rapeseed (Brassica napus L.)

BnA10.LMI1 positively regulates the development of leaf lobes in Brassica napus, and cis-regulatory divergences cause the different allele effects. Leaf shape is an important agronomic trait, and large variations in this trait exist within the Brassica germplasm. The lobed leaf is a unique morphological characteristic for Brassica improvement. Nevertheless, the molecular basis of leaf lobing in Brassica is poorly understood. Here, we show that an incompletely dominant locus, BnLLA10, is responsible for the lobed-leaf shape in rapeseed. A LATE MERISTEM IDENTITY1 (LMI1)-like gene (BnA10.LMI1) encoding an HD-Zip I transcription factor is the causal gene underlying the BnLLA10 locus. Sequence analysis of parental alleles revealed no sequence variations in the coding sequences, whereas abundant variations were identified in the regulatory region. Consistent with this finding, the expression levels of BnLMI1 were substantially elevated in the lobed-leaf parent compared with its near-isogenic line. The knockout mutations of BnA10.LMI1 gene were induced using the CRISPR/Cas9 system in both HY (the lobed-leaf parent) and J9707 (serrated leaf) genetic backgrounds. BnA10.LMI1 null mutations in the HY background were sufficient to produce unlobed leaves, whereas null mutations in the J9707 background showed no obvious changes in leaf shape compared with the control. Collectively, our results indicate that BnA10.LMI1 positively regulates the development of leaf lobes in B. napus, with cis-regulatory divergences causing the different allelic effects, providing new insights into the molecular mechanism of leaf lobe formation in Brassica crops.

Soil Microbial Resources for Improving Fertilizers Efficiency in an Integrated Plant Nutrient Management System

Tomorrow's agriculture, challenged by increasing global demand for food, scarcity of arable lands, and resources alongside multiple environment pressures, needs to be managed smartly through sustainable and eco-efficient approaches. Modern agriculture has to be more productive, sustainable, and environmentally friendly. While macronutrients such as nitrogen (N), phosphorus (P), potassium (K), and sulfur (S) supplied by mineral fertilizers are vital to crop production, agriculturally beneficial microorganisms may also contribute directly (i.e., biological N2 fixation, P solubilization, and phytohormone production, etc.) or indirectly (i.e., antimicrobial compounds biosynthesis and elicitation of induced systemic resistance, etc.) to crop improvement and fertilizers efficiency. Microbial-based bioformulations that increase plant performance are greatly needed, and in particular bioformulations that exhibit complementary and synergistic effects with mineral fertilization. Such an integrated soil fertility management strategy has been demonstrated through several controlled and non-controlled experiments, but more efforts have to be made in order to thoroughly understand the multiple functions of beneficial microorganisms within the soil microbial community itself and in interaction with plants and mineral resources. In fact, the combined usage of microbial [i.e., beneficial microorganisms: N2-fixing (NF), P-solubilizing, and P mobilizing, etc.] and mineral resources is an emerging research area that aims to design and develop efficient microbial formulations which are highly compatible with mineral inputs, with positive impacts on both crops and environment. This novel approach is likely to be of a global interest, especially in most N- and P-deficient agro-ecosystems. In this review, we report on the importance of NF bacteria and P solubilizing/mobilizing microbes as well as their interactions with mineral P fertilization in improving crop productivity and fertilizers efficiency. In addition, we shed light on the interactive and synergistic effects that may occur within multi-trophic interactions involving those two microbial groups and positive consequences on plant mineral uptake, crop productivity, and resiliency to environmental constraints. Improving use of mineral nutrients is a must to securing higher yield and productivity in a sustainable manner, therefore continuously designing, developing and testing innovative integrated plant nutrient management systems based on relevant biological resources (crops and microorganisms) is highly required.

Historical Datasets Support Genomic Selection Models for the Prediction of Cotton Fiber Quality Phenotypes Across Multiple Environments

Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there has not been a study to evaluate GS prediction models that may be used for predicting cotton breeding lines across multiple environments. In this study, we evaluated the performance of Bayes Ridge Regression, BayesA, BayesB, BayesC and Reproducing Kernel Hilbert Spaces regression models. We then extended the single-site GS model to accommodate genotype × environment interaction (G×E) in order to assess the merits of multi- over single-environment models in a practical breeding and selection context in cotton, a crop for which this has not previously been evaluated. Our study was based on a population of 215 upland cotton (Gossypium hirsutum) breeding lines which were evaluated for fiber length and strength at multiple locations in Australia and genotyped with 13,330 single nucleotide polymorphic (SNP) markers. BayesB, which assumes unique variance for each marker and a proportion of markers to have large effects, while most other markers have zero effect, was the preferred model. GS accuracy for fiber length based on a single-site model varied across sites, ranging from 0.27 to 0.77 (mean = 0.38), while that of fiber strength ranged from 0.19 to 0.58 (mean = 0.35) using randomly selected sub-populations as the training population. Prediction accuracies from the M×E model were higher than those for single-site and across-site models, with an average accuracy of 0.71 and 0.59 for fiber length and strength, respectively. The use of the M×E model could therefore identify which breeding lines have effects that are stable across environments and which ones are responsible for G×E and so reduce the amount of phenotypic screening required in cotton breeding programs to identify adaptable genotypes.

Genetic dissection of the fuzzless seed trait in Gossypium barbadense

Cotton fibres are single-celled trichomes arising from the epidermal cells of the seed coat and may be either long (lint) or very short (fuzz). The dominant fuzzless N1 of Gossypium hirsutum is a defective allele of the At-subgenome homoeolog of MYB25-like, but the genetic components underlying the recessive fuzzless trait from G. barbadense (Gb) are unknown. We have identified five genetic loci, including a major contributing locus containing MYB25-like_Dt, associated with Gb fuzzless seeds based on genotyping of fuzzy and fuzzless near isogenic lines (NILs) from an interspecies cross (G. barbadense × G. hirsutum). At 3 d post-anthesis when fuzz fibres are initiating, expression of MYB25-like_Dt was significantly lower in fuzzless NILs than in fuzzy seeded NILs, while higher MYB25-like_Dt expression was associated with more seed fuzz across different cotton genotypes. Phenotypic and genotypic analysis of MYB25-like homoeoalleles in cottons showing different fibre phenotypes and their crossing progeny indicated that both MYB25-like_At and MYB25-like_Dt are associated with lint development, and that fuzz development is mainly determined by the expression level of MYB25-like_Dt at ~3 d post-anthesis. Expression of Gb fuzzless seeds depends on genetic background and interactions amongst the multiple loci identified. MYB25-like_Dt is one of the best candidates for N2.

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton-producing and cotton-consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome-wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single-nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty-eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high-resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.

Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array

BACKGROUND

Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.

RESULTS

The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content.

CONCLUSIONS

Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.

Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.)

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.

Insights into Interspecific Hybridization Events in Allotetraploid Cotton Formation from Characterization of a Gene-Regulating Leaf Shape

The morphology of cotton leaves varies considerably. Phenotypes, including okra, sea-island, super-okra, and broad leaf, are controlled by a multiple allele locus, L₂ Okra leaf (L₂°) is an incomplete mutation that alters leaf shape by increasing the length of lobes with deeper sinuses. Using a map-based cloning strategy, we cloned the L₂ locus gene, which encodes a LATE MERISTEM IDENTITY 1 (LMI1)-like transcription factor (GhOKRA). Silencing GhOKRA leads to a change in phenotype from okra to broad leaf. Overexpression of GhOKRA in Arabidopsis thaliana greatly increases the degree of the leaf lobes and changes the leaf shape. Premature termination of translation in GhOKRA results in the production of broad leaves. The sequences of OKRA from diploid progenitor D-genome species, and wild races and domesticated allotetraploid cottons in Gossypium hirsutum show that a premature termination mutation occurred before and after the formation of tetraploid cotton, respectively. This study provides genomic insights into the two interspecific hybridization events: one produced the present broad leaf and another formed okra leaf phenotype with complete OKRA, that occurred during allotetraploid cotton formation.

Cardamine hirsuta: a comparative view

Current advances in developmental genetics are increasingly underpinned by comparative approaches as more powerful experimental tools become available in non-model organisms. Cardamine hirsuta is related to the model plant Arabidopsis thaliana and comparisons between these two experimentally tractable species have advanced our understanding of development and diversity. The power of forward genetics to uncover new biology was evident in the isolation of REDUCED COMPLEXITY, a gene which is present in C. hirsuta but lost in A. thaliana, and shapes crucifer leaf diversity. Transferring two Knotted1-like homeobox genes between C. hirsuta and A. thaliana revealed a constraint imposed by pleiotropy on the evolutionary potential of cis regulatory change to modify leaf shape. FLOWERING LOCUS C was identified as a heterochronic gene that underlies natural leaf shape variation in C. hirsuta.

The Immature Fiber Mutant Phenotype of Cotton (Gossypium hirsutum) Is Linked to a 22-bp Frame-Shift Deletion in a Mitochondria Targeted Pentatricopeptide Repeat Gene

Cotton seed trichomes are the most important source of natural fibers globally. The major fiber thickness properties influence the price of the raw material, and the quality of the finished product. The recessive immature fiber (im) gene reduces the degree of fiber cell wall thickening by a process that was previously shown to involve mitochondrial function in allotetraploid Gossypium hirsutum. Here, we present the fine genetic mapping of the im locus, gene expression analysis of annotated proteins near the locus, and association analysis of the linked markers. Mapping-by-sequencing identified a 22-bp deletion in a pentatricopeptide repeat (PPR) gene that is completely linked to the immature fiber phenotype in 2837 F₂ plants, and is absent from all 163 cultivated varieties tested, although other closely linked marker polymorphisms are prevalent in the diversity panel. This frame-shift mutation results in a transcript with two long open reading frames: one containing the N-terminal transit peptide that targets mitochondria, the other containing only the RNA-binding PPR domains, suggesting that a functional PPR protein cannot be targeted to mitochondria in the im mutant. Taken together, these results suggest that PPR gene Gh_A03G0489 is involved in the cotton fiber wall thickening process, and is a promising candidate gene at the im locus. Our findings expand our understanding of the molecular mechanisms that modulate cotton fiber fineness and maturity, and may facilitate the development of cotton varieties with superior fiber attributes.

Enhancing Integrated Pest Management in GM Cotton Systems Using Host Plant Resistance

Cotton has lost many ancestral defensive traits against key invertebrate pests. This is suggested by the levels of resistance to some pests found in wild cotton genotypes as well as in cultivated landraces and is a result of domestication and a long history of targeted breeding for yield and fiber quality, along with the capacity to control pests with pesticides. Genetic modification (GM) allowed integration of toxins from a bacteria into cotton to control key Lepidopteran pests. Since the mid-1990s, use of GM cotton cultivars has greatly reduced the amount of pesticides used in many cotton systems. However, pests not controlled by the GM traits have usually emerged as problems, especially the sucking bug complex. Control of this complex with pesticides often causes a reduction in beneficial invertebrate populations, allowing other secondary pests to increase rapidly and require control. Control of both sucking bug complex and secondary pests is problematic due to the cost of pesticides and/or high risk of selecting for pesticide resistance. Deployment of host plant resistance (HPR) provides an opportunity to manage these issues in GM cotton systems. Cotton cultivars resistant to the sucking bug complex and/or secondary pests would require fewer pesticide applications, reducing costs and risks to beneficial invertebrate populations and pesticide resistance. Incorporation of HPR traits into elite cotton cultivars with high yield and fiber quality offers the potential to further reduce pesticide use and increase the durability of pest management in GM cotton systems. We review the challenges that the identification and use of HPR against invertebrate pests brings to cotton breeding. We explore sources of resistance to the sucking bug complex and secondary pests, the mechanisms that control them and the approaches to incorporate these defense traits to commercial cultivars.