Bt cotton seed purity in Burkina Faso: status and lessons learnt

[BackgroundSince the commercial release of Bt cotton in Burkina Faso in 2009, the issue of seed purity in producers’ fields has rarely been addressed in an unbiased and objective manner. The potential for contamination of conventional seed varieties with Bt traits and the consequent threat to the continuation of organic cotton production has been documented. However, studies are rare on the varietal purity of Bt cotton seeds, despite the implications for the effectiveness and sustainability of their use.

This paper compensates for the lack of research on the varietal purity of cotton seeds in Burkina Faso by reporting the results of Enzyme linked immunosorbent assay tests collected in 2015 on samples of both conventional and Bt varieties from 646 fields.

[Results] According to the conservative criteria used to declare the presence of a Bt gene in a given variety (more than 10% of seeds of conventional variety exhibit Bt traits, and at least 90% of seeds of Bt variety exhibit Bt traits), seed purity was very questionable for both types of variety. For the supposedly conventional variety, the Cry1Ac gene was observed in 63.6% of samples, the Cry2Ab gene was observed in 59.3% of samples, and both genes were detected in 52.2% of the seed samples. Only 29.3% of the seeds that were supposed to be of conventional type contained no Bt genes. Conversely, for the labeled Bt variety, the Cry1Ac gene was found in only 59.6% of samples, the Cry2Ab gene was found in 53.6% of the samples, and both genes were found in 40.4% of the samples. Finally, for the seeds that were supposed to contain both genes (Bollguard 2), both Cry1Ac and Cry2Ab genes were found in only 40.4% of the samples, only one of the genes was found in 32.4% of the samples, and 27.2% of the seeds in the samples contained neither.

Two factors are responsible for the severe lack of seed purity. First, conventional varieties are being contaminated with Bt traits because of a failure to revise the seed production scheme in Burkina Faso to prevent cross-pollination. Second, the original Bt seeds provided to Burkina Faso lacked varietal purity.

The organic sector plays a very minor role in the cotton sector of Burkina Faso (production of organic cotton totaled 453 t in 2018/2019, out of national cotton production of 183 000 t). Nevertheless, the lack of purity in conventional seed varieties is a threat to efforts to expand certified organic cotton production. The poor presence of Bt proteins in supposed Bt varieties undermines their effectiveness in controlling pests and increases the likelihood of the development of resistance among pest populations.

[Conclusion] Our results show the extent of purity loss when inadequate attention is paid to the preservation of seed purity. Pure conventional seeds could vanish in Burkina Faso, while Bt seeds do not carry the combination of the expected Bt traits. Any country wishing to embark on the use of Bt cotton, or to resume its use, as in the case of Burkina Faso, must first adjust its national seed production scheme to ensure that procedures to preserve varietal purity are enforced. The preservation of varietal purity is necessary to enable the launch or the continuation of identity-cotton production. In addition, the preservation of varietal purity is necessary to ensure the sustainable effectiveness of Bt cotton. In order to ensure that procedures to preserve varietal purity are observed, seed purity must be tested regularly, and test results must be published.


[Title] Bt cotton seed purity in Burkina Faso: status and lessons learnt

[Authors] BOURGOU Larbouga, KARGOUGOU Ester, SAWADOGO Mahamadou and FOK Michel

Journal of Cotton Research 2020, 330

https://doi.org/10.1186/s42397-020-00070-4

Apprehending the potential of BABY BOOM transcription factors to mitigate cotton regeneration and transformation

[Abstract] Since the advent of transgenic technology, the incorporation of gene(s) encoding traits of economic importance in cotton is being practiced worldwide. However, factors like recalcitrant nature of cotton cultivars, in vitro regeneration via tissue culture (especially via somatic embryogenesis), genotype dependency, long and toilsome protocols impede the pace of development of transgenic cotton. Besides that, types and age of explants, media composition, plant growth regulators and other environmental factors affect in vitro cotton regeneration significantly. The studies of genetic control of in vitro regeneration in plants have elucidated the role of certain transcription factor genes that are induced and expressed during somatic embryogenesis. Among these transcription factors, BABY BOOM (BBM) plays a very important role in signal transduction pathway, leading to cell differentiation and somatic embryos formation. The role of BBM has been established in plant cell proliferation, growth and development even without exogenous growth regulators. This review intends to provide an informative summary of regeneration and transformation problems in cotton and the latest developments in utilization of BBM transcription factors in cotton. We believe that the use of BBM will not only ease cotton genetic improvement but will also accelerate cotton breeding programmes.

[Title] Apprehending the potential of BABY BOOM transcription factors to mitigate cotton regeneration and transformation

[Authors] YAVUZ Caner, TILLABOEVA Shakhnozakhan & BAKHSH Allah

Journal of Cotton Research 2020, 329

https://doi.org/10.1186/s42397-020-00071-3

Phenylpropanoid metabolism and pigmentation show divergent patterns between brown color and green color cottons as revealed by metabolic and gene expression analyses

[Background] Naturally-colored cotton has become increasingly popular because of their natural properties of coloration, UV protection, flame retardant, antibacterial activity and mildew resistance. But poor fiber quality and limited color choices are two key issues that have restricted the cultivation of naturally-colored cotton. To identify the possible pathways participating in fiber pigmentation in naturally-colored cottons, five colored cotton accessions in three different color types (with green, brown and white fiber) were chosen for a comprehensive analysis of phenylpropanoid metabolism during fiber development.

[Result] The expression levels of flavonoid biosynthesis pathway genes in brown cotton fibers were significantly higher than those in white and green cotton fibers. Total flavonoids and proanthocyanidin were higher in brown cotton fibers relative to those in white and green cotton fibers, which suggested that the flavonoid biosynthesis pathway might not participate in the pigmentation of green cotton fibers. Further expression analysis indicated that the genes encoding enzymes for the synthesis of caffeic acid derivatives, lignin and lignan were activated in the developing fibers of the green cotton at 10 and 15 days post-anthesis.

[Conclusion] Our results strengthen the understanding of phenylpropanoid metabolism and pigmentation in green and brown cotton fibers, and may improve the breeding of naturally-colored cottons.

[Title] Phenylpropanoid metabolism and pigmentation show divergent patterns between brown color and green color cottons as revealed by metabolic and gene expression analyses

[Authors] LI Zhonghua, SU Qian, XU Mingqi, YOU Jiaqi, KHAN Anam Qadir, LI Junyi, ZHANG Xianlong, TU Lili & YOU Chunyuan

Journal of Cotton Research 2020, 327

https://doi.org/10.1186/s42397-020-00069-x

A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

[Background] Cotton is the world’s largest and most important source of renewable natural fiber. BEL1-like homeodomain (BLH) genes are ubiquitous in plants and have been reported to contribute to plant development. However, there is no comprehensive characterization of this gene family in cotton. In this study, 32, 16, and 18 BLH genes were identified from the G. hirsutumG. arboreum, and G. raimondii genome, respectively. In addition, we also studied the phylogenetic relationships, chromosomal location, gene structure, and gene expression patterns of the BLH genes.

[Result] The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis. Among them, 25 members were assigned to 15 chromosomes. Furthermore, gene structure, chromosomal location, conserved motifs, and expression level of BLH genes were investigated in G. hirsutum. Expression profiles analysis showed that four genes (GhBLH1_3GhBLH1_4GhBLH1_5, and GhBLH1_6) from BLH1 subfamily were highly expressed during the fiber cell elongation period. The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid, but not auxin. Exogenous application of gibberellic acid significantly enhanced GhBLH1_3GhBLH1_4, and GhBLH1_5transcripts. Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment.

[Conclusion] The BLH gene family plays a very important role in many biological processes during plant growth and development. This study deepens our understanding of the role of the GhBLH1gene involved in fiber development and will help us in breeding better cotton varieties in the future.

[Title] A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

[Authors] LIU Cuixia, LI Zhifang, DOU Lingling, Yi YUAN, ZOU Changsong, SHANG Haihong, CUI Langjun & XIAO  Guanghui

Journal of Cotton Research 2020, 326

https://doi.org/10.1186/s42397-020-00068-y

Global identification of genes associated with xylan biosynthesis in cotton fiber

[Background] Mature cotton fiber secondary cell wall comprises largely of cellulose (> 90%) and small amounts of xylan and lignin. Little is known about the cotton fiber xylan biosynthesis by far.

[Result] To comprehensively survey xylan biosynthetic genes in cotton fiber, we identified five IRX9, five IRX10, one IRX14, six IRX15, two FRA8, one PARVUS, eight GUX, four GXM, two RWA, two AXY9, 13 TBL genes by using phylogenetic analysis coupled with expression profile analysis and co-expression analyses. In addition, we also identified two GT61 members, two GT47 members, and two DUF579 family members whose homologs in Arabidopsis were not functionally characterized. These 55 genes were regarded as the most probable genes to be involved in fiber xylan biosynthesis. Further complementation analysis indicated that one IRX10 like and two FRA8 related genes were able to partially recover the irregular xylem phenotype conferred by the xylan deficiency in their respective Arabidopsis mutant. We conclude that these genes are functional orthologs of respective genes that are implicated in GX biosynthesis.

[Conclusion] The list of 55 cotton genes presented here provides not only a solid basis to uncover the biosynthesis of xylan in cotton fiber, but also a genetic resource potentially useful for future studies aiming at fiber improvement via biotechnological approaches.

[Title] Global identification of genes associated with xylan biosynthesis in cotton fiber

[Authors] CHEN Feng, GUO Yanjun, CHEN Li, GAN Xinli, LIU Min, LI Juan & XU Wenliang

Journal of Cotton Research 2020, 325

https://doi.org/10.1186/s42397-020-00063-3

Development and application of perfect SSR markers in cotton

[Background] This study aimed to develop a set of perfect simple sequence repeat (SSR) markers with a single copy in the cotton genome, to construct a DNA fingerprint database suitable for authentication of cotton cultivars. We optimized the polymerase chain reaction (PCR) system for multi-platform compatibility and improving detection efficiency. Based on the reference genome of upland cotton and 10× resequencing data of 48 basic cotton germplasm lines, single-copy polymorphic SSR sites were identified and developed as diploidization SSR markers. The SSR markers were detected by denaturing polyacrylamide gel electrophoresis (PAGE) for initial screening, then fluorescence capillary electrophoresis for secondary screening. The final perfect SSR markers were evaluated and verified using 210 lines from different sources among Chinese cotton regional trials.

[Result] Using bioinformatics techniques, 1 246 SSR markers were designed from 26 626 single-copy SSR loci. Adopting a stepwise (primary and secondary) screening strategy, a set of 60 perfect SSR markers was selected with high amplification efficiency and stability, easy interpretation of peak type, multiple allelic variations, high polymorphism information content (PIC) value, uniform chromosome distribution, and single-copy characteristics. A multiplex PCR system was established with ten SSR markers using capillary electrophoresis detection.

[Conclusion] A set of perfect SSR markers of cotton was developed and a high-throughput SSR marker detection system was established. This study lays a foundation for large-scale and standardized construction of a cotton DNA fingerprint database for authentication of cotton varieties.

[Title] Development and application of perfect SSR markers in cotton

[Authors] WU Yuzhen, HUANG Longyu, ZHOU Dayun, FU Xiaoqiong, LI Chao, WEI Shoujun, PENG Jun & KUANG Meng

Journal of Cotton Research 2020, 321

https://doi.org/10.1186/s42397-020-00066-0

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

[Background] Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Quantitative trait loci (QTL) mapping provides a powerful approach to dissect the molecular mechanism in fiber quality traits. In present study, F14recombinant inbred line (RIL) population was backcrossed to paternal parent for a paternal backcross (BC/P) population, deriving from one upland cotton hybrid. Three repetitive BC/P field trials and one maternal backcross (BC/M) field trial were performed including both two BC populations and the original RIL population.

[Result] In total, 24 novel QTLs are detected for fiber quality traits and among which 13 QTLs validated previous results. Thirty-five QTLs in BC/P populations explain 5.01%–22.09% of phenotype variation (PV). Among the 35 QTLs, 23 QTLs are detected in BC/P population alone. Present study provides novel alleles of male parent for fiber quality traits with positive genetic effects. Particularly, qFS-Chr3–1 explains 22.09% of PV in BC/P population, which increaseds 0.48 cN·tex− 1 for fiber strength. A total of 7, 2, 8, 2 and 6 QTLs explain over 10.00% of PV for fiber length, fiber uniformity, fiber strength, fiber elongation and fiber micronaire, respectively. In RIL population, six common QTLs are detected in more than one environment: qFL-Chr1–2qFS-Chr5–1qFS-Chr9–1qFS-Chr21–1qFM-Chr9–1 and qFM-Chr9–2. Two common QTLs of qFE-Chr2–2(TMB2386-SWU12343) and qFM-Chr9–1 (NAU2873-CGR6771) explain 22.42% and 21.91% of PV. The region between NAU4034 and TMB1296 harbor 30 genes (379 kb) in A05 and 42 genes (49 kb) in D05 for fiber length along the QTL qFL-Chr5–1 in BC/P population, respectively. In addition, a total of 142 and 46 epistatic QTLs and QTL × environments (E-QTLs and QQEs) are identified in recombinant inbred lines in paternal backcross (RIL-P) and paternal backcross (BC/P) populations, respectively.

[Conclusion] The present studies provide informative basis for improving cotton fiber quality in different populations.
[Title] QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

[Authors] MA LingLing, SU Ying, NIE Hushuai, CUI Yupeng, CHENG Cheng, IJAZ Babar & HUA  Jinping

Journal of Cotton Research 2020, 322

https://doi.org/10.1186/s42397-020-00060-6

Overexpressing rice lesion simulating disease 1-like gene (OsLOL1) in Gossypium hirsutum promotes somatic embryogenesis and plant regeneration

[Background] Cotton somatic embryogenesis is difficult or rarely frequent to present, which has limited gene function identification and biotechnological utility. Here, we employed a rice key somatic embryogenesis-related gene, rice lesion simulating disease 1-like gene (OsLOL1), to develop transgenic cotton callus for evaluating its function in ectopic plants.

[Result] Overexpressing OsLOL1 can promote cotton callus to form embryogenic callus, not only shortening time but also increasing transition of somatic callus cells to embryogenic callus cells. And the regenerating plantlets per transgenic OsLOL1 embryogenic callus were significantly higher than those in the control transformed with empty vector. Analysis of physiological and biochemical showed that OsLOL1 can repress cotton superoxide dismutase 1 gene (GhSOD1) expression, possibly resulting in reactive oxidant species (ROS) accumulation in transgenic callus cells. And OsLOL1-overexpressed embryogenic callus exhibited higher α-amylase activity compared with the control, resulting from the promotion of OsLOL1 to cotton amylase 7 gene (GhAmy7) and GhAmy8 expression.

[Conclusion] The data showed that OsLOL1 could be used as a candidate gene to transform cotton to increase its somatic embryogenesis capacity, facilitating gene function analysis and molecular breeding in cotton.
[Title] Overexpressing rice lesion simulating disease 1-like gene (OsLOL1) in Gossypium hirsutum promotes somatic embryogenesis and plant regeneration

[Authors] WANG Zhian, WANG Peng, HU Guang, XIAO Juanli, ZHANG Anhong, LUO Xiaoli & WU Jiahe

Journal of Cotton Research 2020, 319

https://doi.org/10.1186/s42397-020-00062-4

Unraveling the puzzle of the origin and evolution of cotton A-genome

[Abstract] Gossypium hirsutum, the most widely planted cotton species, its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species. To better understand the genetic component of cotton, Huang et al. recently sequenced and assembled the first A1-genome G. herbaceum, and updated the A2-genome G. arboreum and (AD)1-genome G. hirsutum. On the basis of the three reference genomes, they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome.

[Title] Unraveling the puzzle of the origin and evolution of cotton A-genome

[Authors] MA Zhiying

Journal of Cotton Research 3, Article number: 17 (2020)

https://doi.org/10.1186/s42397-020-00056-2

Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway

Journal of Cotton Research

[Background] Verticillium wilt, caused by the soil-borne fungus of Verticillium dahliae Kleb., is one of the most devastating diseases of cotton. The complex mechanism underlying cotton resistance to Verticillium wilt remains uncharacterized. Identifying an endogenous resistance gene may be helpful to control this disease. Previous studies revealed that succinate dehydrogenase (SDH) is involved in reactive oxygen species (ROS)-induced stress signaling pathway that is likely to be triggered by salicylic acid (SA). Here, through the metabolomics and differential expression analyses in wilt-inoculated cotton (Gossypium hirsutum), we noticed that GhSDH1–1gene in cotton may play an important role in the resistance to V. dahlia. Then we reported GhSDH1–1 gene and its functional analysis in relation to the resistance of cotton to V. dahliae.

[Results] The GhSDH1–1 gene in cotton root was significantly up-regulated after V. dahlia inoculation, and its expression level peaked at 12 and 24 h post-infection. SA can also induce the up-regulation of GhSDH1–1. Additionally, the functional analysis showed that GhSDH1–1-silenced cotton was more susceptible to V. dahliae than the control because of the significant decrease in abundance of immune-related molecules and severe damage to the SA-signaling pathway. In Arabidopsis thaliana, high expression of GhSDH1–1 conferred high resistance to V. dahliaeArabidopsis that overexpressed GhSDH1–1 had higher resistance to V. dahliae infection compared with the wild-type.

[Conclusions] Our findings provide new insights into the role of GhSDH1–1; it positively regulates cotton resistance to Verticillium wilt. The regulatory mechanism of GhSDH1–1 is closely related to SA-related signaling pathway.

[Title] Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway
[Authors] ZHANG Xiangyue, FENG Zili, ZHAO Lihong, LIU Shichao, WEI Feng, SHI Yongqiang, FENG Hongjie & ZHU Heqin

https://doi.org/10.1186/s42397-020-00052-6