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Brassinosteroids (BRs) participate in the regulation of plant growth and development through BRI1-EMS-SUPPRESSOR1 (BES1)/BRASSINAZOLE-RESISTANT1 (BZR1) family transcription factors. Cotton (Gossypium hirsutum) fibers are highly elongated single cells, and BRs play a vital role in the regulation of fiber elongation. However, the mode of action on how BR is involved in the regulation of cotton fiber elongation remains unexplored. Here, we generated GhBES1.4 over expression lines and found that overexpression of GhBES1.4 promoted fiber elongation, whereas silencing of GhBES1.4 reduced fiber length. DNA affinity purification and sequencing (DAP-seq) identified 1,531 target genes of GhBES1.4, and five recognition motifs of GhBES1.4 were identified by enrichment analysis. Combined analysis of DAP-seq and RNA-seq data of GhBES1.4-OE/RNAi provided mechanistic insights into GhBES1.4-mediated regulation of cotton fiber development. Further, with the integrated approach of GWAS, RNA-seq, and DAP-seq, we identified seven genes related to fiber elongation that were directly regulated by GhBES1.4. Of them, we showed Cytochrome P450 84A1 (GhCYP84A1) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (GhHMG1) promote cotton fiber elongation. Overall, the present study established the role of GhBES1.4-mediated gene regulation and laid the foundation for further understanding the mechanism of BR participation in regulating fiber development.This is a pre-copyedited, author-produced PDF of an article accepted for publication in Plant Physiology following peer review. The version of record [A brassinosteroid transcriptional regulatory network participates in regulating fiber elongation in cotton. Plant Physiology (2022)] is available online at: https://doi.org/10.1093/plphys/kiac590. Deposited by shareyourpaper.org and openaccessbutton.org. We've taken reasonable steps to ensure this content doesn't violate copyright. However, if you think it does you can request a takedown by emailing help@openaccessbutton.org.

As people form their opinion about gene editing applications in agriculture, they are utilizing social media to seek and share information and opinions on the topic. Understanding how the public discusses this technology will influence the development of effective messaging and practitioner engagement in the conversation. The purpose of this study was to describe the characteristics of Twitter content related to applications of gene editing in agriculture. Social media monitoring facilitated a quantitative, descriptive analysis of public Twitter content related to the topic. A Meltwater social media monitor collected N = 13,189 relevant tweets for analysis, revealing the amount of conversation regarding gene editing in agriculture, the number of contributing Twitter users, and the reach of the conversation which was relatively stable over the life of the study. In contrast, engagement with the topic rose with the sentiment of tweets becoming increasingly positive. News organization accounts had the most reach while a mix of news accounts and personal accounts garnered the greatest engagement. These results demonstrate an opportunity for agricultural and science communicators to create affirmative messaging about gene editing in agriculture delivered through news media Twitter accounts potentially increasing the reach and engagement in the social system and with science communication.

Aflatoxin contamination is a global menace that adversely affects food crops and human health. Peanut seed coat is the outer layer protecting the cotyledon both at pre- and post-harvest stages from biotic and abiotic stresses. The aim of the present study is to investigate the role of seed coat against A. flavus infection. In-vitro seed colonization (IVSC) with and without seed coat showed that the seed coat acts as a physical barrier, and the developmental series of peanut seed coat showed the formation of a robust multilayered protective seed coat. Radial growth bioassay revealed that both insoluble and soluble seed coat extracts from 55-437 line (resistant) showed higher A. flavus inhibition compared to TMV-2 line (susceptible). Further analysis of seed coat biochemicals showed that hydroxycinnamic and hydroxybenzoic acid derivatives are the predominant phenolic compounds, and addition of these compounds to the media inhibited A. flavus growth. Gene expression analysis showed that genes involved in lignin monomer, proanthocyanidin, and flavonoid biosynthesis are highly abundant in 55-437 compared to TMV-2 seed coats. Overall, the present study showed that the seed coat acts as a physical and biochemical barrier against A. flavus infection and its potential use in mitigating the aflatoxin contamination.

Lignin is a natural polymer that is the second most abundant polymer on Earth after cellulose. Lignin is mainly deposited in plant secondary cell walls and is an aromatic heteropolymer primarily composed of three monolignols with significant industrial importance. Lignin plays an important role in plant growth and development, protects from biotic and abiotic stresses, and in the quality of animal fodder, the wood, and industrial lignin products. Accurate estimation of lignin content is essential for both fundamental understanding of the lignin biosynthesis and industrial applications of biomass. The thioglycolic acid (TGA) method is a highly reliable method of estimating the total lignin content in the plant biomass. This method estimates the lignin content by forming thioethers with the benzyl alcohol groups of lignin, which are soluble in alkaline conditions and insoluble in acidic conditions. The total lignin content is estimated using a standard curve generated from commercial bamboo lignin.

Background Male sterility has tremendous scientific and economic importance in hybrid seed production. Identification and characterization of a stable male sterility gene will be highly beneficial for making hybrid seed production economically feasible. In soybean, eleven male-sterile, female-fertile mutant lines (ms1, ms2, ms3, ms4, ms5, ms6, ms7, ms8, ms9, msMOS, and msp) have been identified and mapped onto various soybean chromosomes, however the causal genes responsible for male sterility are not isolated. The objective of this study was to identify and functionally characterize the gene responsible for the male sterility in the ms4 mutant. Results The ms4 locus was fine mapped to a 216 kb region, which contains 23 protein-coding genes including Glyma.02G243200, an ortholog of Arabidopsis MALE MEIOCYTE DEATH 1 (MMD1), which is a Plant Homeodomain (PHD) protein involved in male fertility. Isolation and sequencing of Glyma.02G243200 from the ms4 mutant line showed a single base insertion in the 3rd exon causing a premature stop codon resulting in truncated protein production. Phylogenetic analysis showed presence of a homolog protein (MS4_homolog) encoded by the Glyma.14G212300 gene. Both proteins were clustered within legume-specific clade of the phylogenetic tree and were likely the result of segmental duplication during the paleoploidization events in soybean. The comparative expression analysis of Ms4 and Ms4_homologs across the soybean developmental and reproductive stages showed significantly higher expression of Ms4 in early flowering (flower bud differentiation) stage than its homolog. The functional complementation of Arabidopsis mmd1 mutant with the soybean Ms4 gene produced normal stamens, successful tetrad formation, fertile pollens and viable seeds, whereas the Ms4_homolog was not able to restore male fertility. Conclusions Overall, this is the first report, where map based cloning approach was employed to isolate and characterize a gene responsible for the male-sterile phenotype in soybean. Characterization of male sterility genes may facilitate the establishment of a stable male sterility system, highly desired for the viability of hybrid seed production in soybean. Additionally, translational genomics and genome editing technologies can be utilized to generate new male-sterile lines in other plant species. Electronic supplementary material The online version of this article (10.1186/s12870-019-1979-4) contains supplementary material, which is available to authorized users.

Proline-rich extensin-like receptor protein kinases (PERKs) are known for their roles in the developmental processes and stress responses of many plants. We have identified 30 TaPERK genes in the genome of T. aestivum, exploring their evolutionary and syntenic relationship and analyzing their gene and protein structures, various cis-regulatory elements, expression profiling, and interacting miRNAs. The TaPERK genes formed 12 homeologous groups and clustered into four phylogenetic clades. All the proteins exhibited a typical domain organization of PERK and consisted of conserved proline residue repeats and serine-proline and proline-serine repeats. Further, the tyrosine-x-tyrosine (YXY) motif was also found conserved in thirteen TaPERKs. The cis-regulatory elements and expression profiling under tissue developmental stages suggested their role in plant growth processes. Further, the differential expression of certain TaPERK genes under biotic and abiotic stress conditions suggested their involvement in defense responses as well. The interaction of TaPERK genes with different miRNAs further strengthened evidence for their diverse biological roles. In this study, a comprehensive analysis of obtained TaPERK genes was performed, enriching our knowledge of TaPERK genes and providing a foundation for further possible functional analyses in future studies.

Background Producing rainfed cotton (Gossypium hirsutum L.) with high fiber quality has been challenging in the Texas High Plains because of extended periods of insufficient rainfall during sensitive boll developmental stages. Genetic variation created by Ethyl MethaneSulfonate (EMS) mutagen has successfully improved fiber quality of cotton. However, little is known about the effect of water deficit environments on fiber quality. Three EMS treated populations were advanced from the first to the fourth generation (M1 to M4) as bulk harvested populations. In 2014, single-plant divergent selection was applied based on perceived morphological and agronomic differences seen during and at the end of the season. Results Analyses from these selections in 2014–2016 showed significant (P

Cellulose is the most abundant polymer on Earth generated by photosynthesis and the main load-bearing component of cell walls. The cell wall plays a significant role in plant growth and development by providing strength, rigidity, rate and direction of cell growth, cell shape maintenance, and protection from biotic and abiotic stressors. The cell wall is primarily composed of cellulose, lignin, hemicellulose and pectin. Recently plant cell walls have been targeted for the second-generation biofuel and bioenergy production. Specifically, the cellulose component of the plant cell wall is used for the production of cellulosic ethanol. Estimation of cellulose content of biomass is critical for fundamental and applied cell wall research. The Updegraff method is simple, robust, and the most widely used method for the estimation of crystalline cellulose content of plant biomass. The alcohol insoluble crude cell wall fraction upon treatment with Updegraff reagent eliminates the hemicellulose and lignin fractions. Later, the Updegraff reagent resistant cellulose fraction is subjected to sulfuric acid treatment to hydrolyze the cellulose homopolymer into monomeric glucose units. A regression line is developed using various concentrations of glucose and used to estimate the amount of the glucose released upon cellulose hydrolysis in the experimental samples. Finally, the cellulose content is estimated based on the amount of glucose monomers by colorimetric anthrone assay.

Main conclusion A novel inducible secretion system mutation in Sorghum named Red root has been identified. The mutant plant root exudes pigmented compounds that enriches Actinobacteria in its rhizosphere compared to BTx623. Abstract Favorable plant–microbe interactions in the rhizosphere positively influence plant growth and stress tolerance. Sorghum bicolor, a staple biomass and food crop, has been shown to selectively recruit Gram-positive bacteria (Actinobacteria) in its rhizosphere under drought conditions to enhance stress tolerance. However, the genetic/biochemical mechanism underlying the selective enrichment of specific microbial phyla in the sorghum rhizosphere is poorly known due to the lack of available mutants with altered root secretion systems. Using a subset of sorghum ethyl methanesulfonate (EMS) mutant lines, we have isolated a novel Red root (RR) mutant with an increased accumulation and secretion of phenolic compounds in roots. Genetic analysis showed that RR is a single dominant mutation. We further investigated the effect of root-specific phenolic compounds on rhizosphere microbiome composition under well-watered and water-deficit conditions. The microbiome diversity analysis of the RR rhizosphere showed that Actinobacteria were enriched significantly under the well-watered condition but showed no significant change under the water-deficit condition. BTx623 rhizosphere showed a significant increase in Actinobacteria under the water-deficit condition. Overall, the rhizosphere of RR genotype retained a higher bacterial diversity and richness relative to the rhizosphere of BTx623, especially under water-deficit condition. Therefore, the RR mutant provides an excellent genetic resource for rhizosphere-microbiome interaction studies as well as to develop drought-tolerant lines. Identification of the RR gene and the molecular mechanism through which the mutant selectively enriches microbial populations in the rhizosphere will be useful in designing strategies for improving sorghum productivity and stress tolerance.

Plant small RNAs (sRNAs) and/or double-stranded RNAs (dsRNAs) trigger RNA interference (RNAi) in interacting eukaryotic pathogens or parasites. However, it is unknown whether this phenomenon could operate in bacterial phytopathogens, which lack a eukaryotic-like RNAi machinery. Here, we first show that Arabidopsis-encoded inverted repeat transgenes trigger silencing ofPseudomonas syringaeheterologous reporter and endogenous virulence-associated genes during infection. Antibacterial Gene Silencing (AGS) of the latter was associated with a reduced pathogenesis, which was also observed upon application of corresponding plant-derived RNAs onto wild-type plants prior to infection. We additionally demonstrate that sRNAs directed against virulence factor transcripts were causal for silencing and pathogenesis reduction, while cognate long dsRNAs were inactive. Overall, this study provides the first evidence that plant sRNAs can directly reprogram gene expression in a phytopathogenic bacterium and may have wider implications in the understanding of how plants regulate transcriptome, community composition and genome evolution of associated bacteria.

Protein kinases play fundamental roles in plant development and environmental stress responses. Here, we identified the STRESS INDUCED FACTOR (SIF) gene family, which encodes four leucine-rich repeat receptor-like protein kinases in Arabidopsis (Arabidopsis thaliana). The four genes, SIF1 to SIF4, are clustered in the genome and highly conserved, but they have temporally and spatially distinct expression patterns. We employed Arabidopsis SIF knockout mutants and overexpression transgenics to examine SIF involvement during plant pathogen defense. SIF genes are rapidly induced by biotic or abiotic stresses, and SIF proteins localize to the plasma membrane. Simultaneous knockout of SIF1 and SIF2 led to improved plant salt tolerance, whereas SIF2 overexpression enhanced PAMP-triggered immunity and prompted basal plant defenses, significantly improving pathogen resistance. Furthermore, SIF2 overexpression plants exhibited up-regulated expression of the defense-related genes WRKY53 and flg22-INDUCED RECEPTOR-LIKE KINASE1 as well as enhanced MPK3/MPK6 phosphorylation upon pathogen and elicitor treatments. The expression of the calcium signaling-related gene PHOSPHATE-INDUCED1 also was enhanced in the SIF2-overexpressing lines upon pathogen inoculation but repressed in the sif2 mutants. Bimolecular fluorescence complementation demonstrates that the BRI1-ASSOCIATED RECEPTOR KINASE1 protein is a coreceptor of the SIF2 kinase in the signal transduction pathway during pathogen invasion. These findings characterize a stress-responsive protein kinase family and illustrate how SIF2 modulates signal transduction for effective plant pathogenic defense.

The non-renewability and greenhouse gas emission nature of crude oil led to the use of renewable plant-based biofuels as alternative energy. Sweet sorghum offers one of the best plant-based bioethanol production from its sugary stalk. Identification and mapping of quantitative trait loci associated with sugar-related traits in sorghum is a crucial step toward the improvement of the sugar content of the crop. The present study was carried out to identify and map QTLs associated with °Brix, stalk diameter and plant height using F2:3 segregating mapping populations derived from a cross between grain sorghum (Sorcoll 163) and sweet sorghum (Gambella). Phenotypic evaluation was conducted in two different environments. A genetic map was constructed using 192 F2 populations genotyped using 76 SSR markers. Estimated heritability for °Brix, stem diameter and plant height amounted to 0.88, 0.41 and 0.65, respectively. A total of seven QTLs distributed across five linkage groups that controls °Brix content were detected using Inclusive Composite Interval Mapping. Each QTL contributed 17.2–44.3% of the total phenotypic variation. The two QTLs located on linkage group SBI-05 and SBI-06 repeated in both environments. These QTLs can be the target of the breeding programs in the future due to high heritability as well as stability in two different environments. The number of SSR markers used in present study is relatively fewer and fine mapping of the target regions should be considered in order to further dissecting the region. All the detected QTLs in this study are categorized as major QTLs, and it could be used further in sweet sorghum improvement program.

Sorghum is among the most important cereal crops produced globally due to its drought tolerance nature and multiple uses. Ethiopia is endowed with high genetic diversity for sorghum and the main sources of several genes that are responsible for biotic and abiotic stress tolerance. Despite this potential, sorghum productivity in the country remains very low. The study was designed to screen and compile the best simple sequence repeats (SSRs) that can be used for marker-assisted breeding of sorghum. Out of a total 304 SSRs markers screened used across eleven farmers preferred sorghum genotypes, nearly half of the markers 139 (45.7%) detected 543 alleles and a high degree of polymorphic information content (PIC) averaging 0.53. The overall observed heterozygosity (Ho) across all loci varied from 0.00 to 1.00 with an average of 0.16. Nearly 60 % (83 markers) showed no Ho. The gene diversity index (expected heterozygosity, He) ranged from 0.17 to 0.91 with a mean of 0.58. The weighted neighbor-joining cluster analysis grouped the genotypes into three distinct groups. All genotypes with stay-green features (B 35, Sorcoll 163/07, E 36-1 and Sorcoll 141/07) were clustered together. Genotypes such as Gambella, Macia, 76T#23 and Meko were clustered in the second group. The third group consists of Teshale and Sorcoll 146/07. Most of the used SSR markers were linked with stay-green traits and successfully discriminated genotypes with stay green (cluster I) from those genotypes with non-stay green features (cluster II and III). The result reveals the potential application of microsatellites in Ethiopian marker-assisted breeding program for further characterization and/or mapping of targeted traits in sorghum.

Cellulose synthesis is precisely regulated by internal and external cues, and emerging evidence suggests that light regulates cellulose biosynthesis through specific light receptors. Recently, the blue light receptor CRYPTOCHROME 1 (CRY1) was shown to positively regulate secondary cell wall biosynthesis in Arabidopsis (Arabidopsis thaliana). Here, we characterize the role of FLAVIN-BINDING KELCH REPEAT, F-BOX 1 (FKF1), another blue light receptor and well-known photoperiodic flowering time regulator, in cellulose biosynthesis. A phenotype suppression screen using a cellulose deficient mutant cesa1(aegeus),cesa3(ixr1-2) (c1,c3), which carries nonlethal point mutations in CELLULOSE SYNTHASE A 1 (CESA1) and CESA3, resulted in identification of the phenotype-restoring large leaf (llf) mutant. Next-generation mapping using the whole genome resequencing method identified the llf locus as FKF1. FKF1 was confirmed as the causal gene through observation of the llf phenotype in an independent triple mutant c1,c3,fkf1-t carrying a FKF1 T-DNA insertion mutant. Moreover, overexpression of FKF1 in llf plants restored the c1,c3 phenotype. The fkf1 mutants showed significant increases in cellulose content and CESA gene expression compared with that in wild-type Columbia-0 plants, suggesting a negative role of FKF1 in cellulose biosynthesis. Using genetic, molecular, and phenocopy and biochemical evidence, we have firmly established the role of FKF1 in regulation of cellulose biosynthesis. In addition, CESA expression analysis showed that diurnal expression patterns of CESAs are FKF1 independent, whereas their circadian expression patterns are FKF1 dependent. Overall, our work establishes a role of FKF1 in the regulation of cell wall biosynthesis in Arabidopsis.

Plant synthetic biology is a rapidly growing field of science which is expected to significantly contribute to the food, fiber, and fuel deficit because of fast increasing world population. By combining the fundamental understanding of plant biology with technological advancement and genetic engineering principles, plant synthetic biology is poised to play a major role in accelerating the development of novel agronomical traits. The recent development of efficient design and modeling-related computational tools, improved DNA synthesis and assembly technologies to generate complicated DNA constructs, and cutting-edge next-generation sequencing technologies have reduced many of the obstacles of plant synthetic biology. In this chapter we have discussed the principles, methods of synthetic biology, and tools that can be applied to engineer various stages of central dogma keeping plant synthetic biology in perspective. We have also focused on the future applications and challenges of plant synthetic biology.

Figure S1. Sequence comparison of the genomic DNA sequences showed an insertion of a single nucleotide â Aâ in the 3rd exon of the Ms4 gene (Glyma.02G243200) in the male-sterile (ms4/ms4) line. Green color boxes represent exonic sequences. Insertion mutation is shown by black color box. Figure S2. Amino acid alignment showing a frameshift mutation resulted in an early stop codon in ms4 sterile mutant. The resulting truncated protein lacks the Plant Homeodomain (PHD) which is otherwise present at the C-terminus of native MS4 protein. Figure S3. Sequence comparison of the soybean Ms4 and Ms4_homolog coding sequences. Figure S4. Similarity comparison of the soybean MS4 and MS4_homolog amino acid sequences. Figure S5. Heatmap representing the expression of the remaining 22 genes present in the mapped region. Figure S6. Constructs used for the complementation purposes. (A) Arabidopsis MMD1 native promoter driven genomic and CDS Ms4 constructs. (B) Arabidopsis MMD1 native promoter driven genomic and CDS Ms4_homolog constructs. Table S1. A list of 23 predicted genes in the ms4 region flanked by BARCSOYSSR_02_1515 and BARCSOYSSR_02_ 1528. Table S2. Details of primers used in present study for various purposes. Table S3. Duplication gene list of syntenic block 245 between soybean chr02-chr14 with Ms4 and Ms4_homolog as duplicated gene pair (highlighted in yellow). Table S4. List of SRA files used for the expression analysis of Ms4 and Ms4_h. (PDF 672 kb)

Background Auxin-induced genes regulate many aspects of plant growth and development. The Gretchen Hagen 3 (GH3) gene family, one of three major early auxin-responsive families, is ubiquitous in the plant kingdom and its members function as regulators in modulating hormonal homeostasis, and stress adaptations. Specific Auxin-amido synthetase activity of GH3 subfamily II genes is reported to reversibly inactivate or fully degrade excess auxin through the formation of amino acid conjugates. Despite these crucial roles, to date, genome-wide analysis of the GH3 gene family has not been reported in cotton. Results We identified a total of 10 GH3 subfamily II genes in G. arboreum, 10 in G. raimondii, and 20 in G. hirsutum, respectively. Bioinformatic analysis showed that cotton GH3 genes are conserved with the established GH3s in plants. Expression pattern analysis based on RNA-seq data and qRT-PCR revealed that 20 GhGH3 genes were differentially expressed in a temporally and spatially specific manner, indicating their diverse functions in growth and development. We further summarized the organization of promoter regulatory elements and monitored their responsiveness to treatment with IAA (indole-3-acetic acid), SA (salicylic acid), GA (gibberellic acid) and BL (brassinolide) by qRT-PCR in roots and stems. These hormones seemed to regulate the expression of GH3 genes in both a positive and a negative manner while certain members likely have higher sensitivity to all four hormones. Further, we tested the expression of GhGH3 genes in the BR-deficient mutant pag1 and the corresponding wild-type (WT) of CCRI24. The altered expression reflected the true responsiveness to BL and further suggested possible reasons, at least in part, responsible for the dramatic dwarf and shriveled phenotypes of pag1. Conclusion We comprehensively identified GH3 subfamily II genes in cotton. GhGH3s are differentially expressed in various tissues/organs/stages. Their response to IAA, SA, BL and GA and altered expression in pag1 suggest that some GhGH3 genes might be simultaneously involved in multiple hormone signaling pathways. Taken together, our results suggest that members of the GhGH3 gene family could be possible candidate genes for mechanistic study and applications in cotton fiber development in addition to the reconstruction of plant architecture. Electronic supplementary material The online version of this article (10.1186/s12870-018-1545-5) contains supplementary material, which is available to authorized users.

Here we report a practical and efficient method for the synthesis of menaquinone vitamin (K2) analog MK-6 in all trans forms through “1 + 5 convergent synthetic approach” of pentaprenyl chloride with monoprenyl menadione derivative. In the synergistic factors, less efficient leaving group/more efficient nucleophile (Cl) in the substrate makes it more prominent reaction by eliminating all Sn2’ side reaction products. Further, the addition of acetic acid in the last step (desulfonation) of reaction sequence removes the limitations of the reactions in terms of cyclized side product (multiple reactions of pentaprenyl alcohol with Et3B), byproduct (Et3B, incendiary compound) formations and their interruption in the tricky purification processes. The utility of this method was further extended to find an efficient one-pot synthesis to MK-9 to the gram scale synthesis. This approach is economical and efficient and avoids the awkward chromatographic separation processes.

Aflatoxins, which have been classified as a group-1 carcinogen are the well-known mycotoxins produced by Aspergillus flavus. Aflatoxins have been linked to liver diseases, acute hepatic necrosis, resulting in cirrhosis or hepatocellular carcinomas due to which it incurs a loss of value in international trade for peanuts contaminated with it. The four main aflatoxins are B1, B2, G1, and G2 of which B1 is predominant. In plants, the cell wall is the primary barrier against pathogen invasion. Cell wall fortifications such as deposition of callose, cellulose, lignin, phenolic compounds and structural proteins help to prevent the pathogen infection. Further, the host cell’s ability to rapidly repair and reinforce its cell walls will result in a reduction of the penetration efficiency of the pathogen. Peanut seed coat acts as a physical and biochemical cell wall barrier against both pre and post-harvest pathogen infection. The structure of seed coat and the presence of polyphenol compounds have been reported to inhibit the growth of A. flavus, however, not successfully employed to develop A. flavus resistance in peanut. A comprehensive understanding of peanut seed coat development and biochemistry will provide information to design efficient strategies for the seed coat mediated A. flavus resistance and Aflatoxin contamination.

The Texas High Plains often has extended periods between rainfall events, which can lead to a reduction in the yield and fiber quality of cotton (Gossypium hirsutum L.). It is known that cultivated cotton suffers from low levels of genetic diversity due to the over-use in breeding of similar gene pools, which may hinder breeding for drought tolerance. In this study, for the first time the novel variability or genetic diversity of morphological and agronomic traits possibly created by the chemical mutagen ethyl methanesulfonate (EMS) was evaluated to improve drought tolerance in cotton by traits’ response to different irrigation regimes. EMS is a chemical mutagen that has been shown to cause point mutations in the DNA of many model plants and crop species. Three EMS treated lines were advanced from the M1 to M4 generation as bulk-harvested populations. A diverse selection scheme was applied to capture most of the genetic trait-variability or diversity and superior lines in these populations. In 2014–2016 the diversity of these populations was evaluated based on four agronomic and thirteen morphological traits to determine differences in response to multiple irrigation rates. Analyses of these traits showed statistically significant (p ≤ 0.05) differences between and within populations when compared to the original non-treated EMS source, with most of the variability being observed in the high irrigation rate. However, none of the EMS treated populations had significantly (p ≤ 0.05) better lint yield than the commercial cultivar (control) in 2016. EMS yield performance was possibly constrained by the applied diverse selection scheme of this study. Traits such as total number of bolls, bolls retained at node 7 and below, and those retained between nodes 8 and 12, and bolls retained at node of first fruiting branch may be predictors to improve cotton production (yield) in water limiting environments.

Plant photosynthetic pigments are important in harvesting the light energy and transfer of energy during photosynthesis. There are several yellow foliar mutants discovered in soybean and chromosomal locations for about half of them have been deduced. Viable-yellow mutants are capable of surviving with decreased photosynthesis, while lethal-yellow mutants die shortly after germination. In addition to the decreased chlorophyll content, other features associated with yellow mutants include altered Chl a and Chl b ratio, reduction in chloroplast size and number, lower levels of other photosynthetic pigments, inability of thylakoids to stack into granum, lack of lamellae to interconnect granum and reduced size of the light harvesting complex. For some yellow mutants, temperature and/or light play a critical role in the manifestation of phenotype. Although yellow foliar mutants are viewed as undesirable for crop production, there is the possibility of these mutants to create a positive impact by reducing the total amount of chlorophyll and diverting resources toward increased biochemical photosynthetic capacity leading to increased yield. Recent advances in model plants led to the isolation and characterization of various genes associated with yellow foliar phenotype. Knowledge gained from the model plants can be applied using homology based cloning approach to isolate genes in soybean and understanding the modes of actions of the involved proteins. Identifying and characterizing yellow foliar mutants will not only aid in understanding the biosynthetic pathways involved in the photosynthetic machinery, but may also provide ways to increase soybean productivity.

Data S1. Protein alignment of AtSIFs and GhLRR-RLKs. (PDF 2711Â kb)

Figure S3. Multiple sequence alignment of 20 GhGH3s. (PDF 35â kb)

Figure S5. Expression of GhGH3 gene family in response to IAA, SA, BL and GA treatment. R, roots; S, stems. The expression pattern of each GhGH3 gene in response to IAA, SA, BL and GA treatment is also shown. (PDF 1630â kb)