Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Background Cotton is an economically important crop.It is crucial to find an effective method to improve cotton yield,and one approach is to decrease the abscission of cotton bolls and buds.However,the lack of knowledge of the genetic and molecular mechanisms underlying cotton boll abscission traits has hindered genetic improvements.Results Pearson’s correlation analysis revealed a significant positive correlation between boll abscission rates 1(AR1)and boll abscission rates 2(AR2).A genome-wide association study was conducted on 145 loci that exhibited high polymorphism and were uniformly distributed across 26 chromosomes(pair).The study revealed 18,46,and 62 markers that were significantly associated with boll abscission,fiber quality,and yield traits(P<0.05),explaining 1.75%–7.13%,1.16%–9.58%,and 1.40%–5.44%of the phenotypic variation,respectively.Notably,the marker MON_SHIN-1584b was associated with the cotton boll abscission trait,whereas MON_CGR5732a was associated with cotton boll abscission and fiber quality traits.Thirteen of the marker loci identified in this study had been previously reported.Based on phenotypic effects,six typical cultivars with elite alleles related to cotton boll abscission,fiber quality,and yield traits were identified.These cultivars hold great promise for widespread utilization in breeding programs.Conclusions These results lay the foundation for understanding the molecular regulatory mechanism of cotton boll abscission and provide data for the future improvement of cotton breeding.

Correction:Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Correction:J Cotton Res 7,20(2024)https://doi.org/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published article.1.One of the author’s name has been corrected from Gou Chunping to Guo Chunping.2.The reference(Zhao SQ.2016)in Table 2 has been updated to:Zhao SQ.Analysis on the major gene and multigene mixed inheritance and QTL mapping for early maturity traits in upland cotton.Chin Acad Agric Sci.2016.https://doi.org/10.3969/j.issn.201600501.(in Chinese with English abstract).3.In’Results’part,’Phenotype analysis of 238 cotton boll abscission among cotton accessions’paragraph,the phenotype analysis of AR1 ranging from 19.27%–63.79%,which was wrongly written as 19.27%-63.97%.4.The‘2018KRL’is modified to‘2018KEL’in Table 1.

Identification of candidate genes for aphid resistance in upland cotton by QTL mapping and expression analysis

Lignin is one of the main components of cell walls and is essential for resistance to insect pests in plants.Cotton plants are damaged by aphid(Aphis gossypii) worldwide but resistant breeding is undeveloped due to scarce knowledge on resistance genes and the mechanism. This study reported a lignin biosynthesisrelated gene identified in the F_(2) population derived from the cross between cotton cultivars Xinluzao 61(resistant to aphid) and Xinluzao 50(susceptible to aphid). A quantitative trait locus was mapped on chromosome D04 with a logarithm of odds(LOD) score of 5.99 and phenotypic effect of 27%. RNA-seq analysis of candidate intervals showed that the expression level of GH_D04G1418 was higher in the resistant cultivar than in the susceptible cultivar. This locus is close to AtLAC4 in the phylogenetic tree and contains a conserved laccase domain. Hence, it was designated GhLAC4-3. Silencing of GhLAC4-3 in Xinluzao 61 via virus-induced gene silencing(VIGS) resulted in decreased lignin content and increased susceptibility to aphids. These results suggest that GhLAC4-3 might enhance aphid resistance by regulating lignin biosynthesis in cotton.

Effects of cotton field management practices on soil CO2 emission and C balance in an arid region of Northwest China

Changes in both soil organic C storage and soil respiration in farmland ecosystems may affect atmospheric CO2 concentration and global C cycle. The objective of this field experiment was to study the effects of three crop field management practices on soil CO2 emission and C balance in a cotton field in an arid region of Northwest China. The three management practices were irrigation methods（drip and flood）, stubble managements（stubble-incorporated and stubble-removed） and fertilizer amendments（no fertilizer（CK）, chicken manure（OM）, inorganic N, P and K fertilizer（NPK）, and inorganic fertilizer plus chicken manure（NPK＋OM））. The results showed that within the C pool range, soil CO2 emission during the whole growing season was higher in the drip irrigation treatment than in the corresponding flood irrigation treatment, while soil organic C concentration was larger in the flood irrigation treatment than in the corresponding drip irrigation treatment. Furthermore, soil CO2 emission and organic C concentration were all higher in the stubble-incorporated treatment than in the corresponding stubble-removed treatment, and larger in the NPK＋OM treatment than in the other three fertilizer amendments within the C pool range. The combination of flood irrigation, stubble incorporation and application of either NPK＋OM or OM increased soil organic C concentration in the 0-60 cm soil depth. Calculation of net ecosystem productivity（NEP） under different management practices indicated that the combination of drip irrigation, stubble incorporation and NPK＋OM increased the size of the C pool most, followed by the combination of drip irrigation, stubble incorporation and NPK. In conclusion, management practices have significant impacts on soil CO2 emission, organic C concentration and C balance in cotton fields. Consequently, appropriate management practices, such as the combination of drip irrigation, stubble incorporation, and either NPK＋OM or NPK could increase soil C storage in cotton fields of Northwest China.

Estimating Aboveground Fresh Biomass of Different Cotton Canopy Types with Homogeneity Models Based on Hyper Spectrum Parameters

AGB （aboveground fresh biomass） is one of the most important parameters of the crop condition monitored with remote sensing. Hyper spectrum remote sensing with the fine spectrum information becomes the efficient method estimating the vegetation AGB. The research was conducted in Xinjiang, the largest cotton planting region of China. The paper analyzed the correlation between the cotton AGB and reflective spectrum and the first derivative spectrum, and the variation coefficient of the waveband reflectance. According to the analysis above, all of 23 parameters, including the hyper spectrum reflectance, the first derivative spectrum parameters and normalization vegetation indexes, were established. And then the estimation models on cotton AGB of relaxing and compact canopy type were established and tested respectively. The tested results showed that Fgo1, [901,502], [901,629], [901,672] among the reflective spectral parameters and D525, D956, D1019, D1751 among the first derivative spectral parameters had the homogenous effect on different cotton canopy types, and the determination coefficients of the models above all arrive at the significant level of 0.99 confidence interval. At last, the tested results of the homogeneity models for different canopy types indicated the parameters of [901, 502], [901,629], [901,672] have more satisfying veracity than others, and the relative errors are as low as 17.0, 16.3 and 16.7% correspondingly; in contrast, the estimation veracity of the first derivative spectrum parameters of single waveband is low.

Genome-wide association mapping of stress-tolerance traits in cotton

Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate(RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt(the relative germination rates of seeds under salt stress),RGR-Cold(the relative germination rates of seeds under cold stress), and DIV(the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP(best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs(i02237 Gh, i02243 Gh)on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval(D01, 37771–1942912). Of these four genes,GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton.

Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

Background: Cotton fiber yield is a complex trait,which can be influenced by multiple agronomic traits.Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton.Results: In this study,503 upland cotton varieties covering the four breeding stages(BS1–BS4,1911–2011)in China were used for association mapping and domestication analysis.One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified,among which,29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4,and 26 markers showed decreased trend effect.Four favorable alleles of 9 major loci(R^(2)≥3)were strongly selected during the breeding stages,and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data.Conclusions :The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China.

Advances and prospects of genetic mapping of Verticillium wilt resistance in cotton

Verticillium wilt is one of the most important diseases affecting cotton production in China.The fungus,Verticillium dahliae,has a wide host range and a high degree of genetic variability.No resistance resources have been found in the available planting resources,thus presenting difficulties and challenges for our study.The long-term production practice shows that selection of disease-resistant varieties is the most economical and effective measure to control Verticillium wilt of cotton to reduce the yield loss and quality decline of cotton.In this paper,we summarized the genetic mapping population,the analysis method of genetic localization,the discovery,mining and cloning of disease-resistant quantitative trait loci/markers,and the analysis of their genetic functions,so as to provide information for the molecular breeding approach of disease-resistant cotton.

Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL,significant SNP and transcriptomic data

Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

Developmental Threshold Temperature and Effective Accumulated Temperature of Potosia brevitarsis Lewis

[ Objective] The paper was to study the relationship between temperature and development of Potosia brevitarsis Lewis. [ Methods] Six constant tem- peratures （21, 24, 27, 30, 33 and 36 ℃ ） were set in the laboratory to study developmental threshold temperature and effective accumulated temperature of P. brevitarsis. [ Result] The developmental durations of various states of P. brevitarsis were shortened with the increasing temperature ranged from 21 ℃ to 36 ℃ ; the developmental rates were accelerated with the increasing temperature. The developmental threshold temperatures of egg, larva, pupa and pre-ovipesition of adult were estimated to be 12.79, 9.15, 14.86 and 13.80 ℃, respectively; the effective accumulated temperature were 136.25, 3 031.31,308.92 and 98.35 d · ℃, respectively. The developmental threshold temperature and effective amcumulated temperature for one complete generation were 9.96 ℃ and 3 628.73 d · ℃, re- spectively. Combined with meteorological data, the theoretical generation number of P. brevitarsis occurred in Shihezi was presumed to be one per year, which was basically coincided with actual occurrence generations in fields. [ Conclusion] The paper provided theoretical basis for effective control against P. brevitarsis.

Morphological and cytological assessments reveal pollen degradation causes pollen abortion in cotton cytoplasmic male sterility lines

Background Understanding the mechanism of male sterility is crucial for producing hybrid seeds and developing sterile germplasm resources.However,only a few cytoplasmic male sterility(CMS)lines of cotton have been produced due to several challenges,like inadequate variation of agronomic traits,incomplete sterility,weak resilience of restorer lines,and difficulty in combining strong dominance.Therefore,the morphological and cytological identification of CMS in cotton will facilitate hybrid breeding.Results Two F_(2) segregating populations of cotton were constructed from cytoplasmic male sterile lines(HaA and 01A,maternal)and restorer lines(HaR and 26R,paternal).Genetic analysis of these populations revealed a segregation ratio of 3:1 for fertile to sterile plants.Phenotypic analysis indicated no significant differences in traits of flower bud development between sterile and fertile plants.However,sterile plants exhibited smaller floral organs,shortened filament lengths,and anther atrophy on the flowering day in comparison with the fertile plants.When performed scanning electron microscopy(SEM),the two F_(2) populations revealed morphological variations in the anther epidermis.Cellular analysis showed no significant differences in pollen development before pollen maturation.Interestingly,between the pollen maturation and flowering stages,the tapetum layer of sterile plants degenerated prematurely,resulting in abnormal pollen grains and gradual pollen degradation.Conclusion The results of this study suggest that fertility-restoring genes are controlled by a single dominant gene.Sterile plants exhibit distinctive floral morphology,which is characterized by stamen atrophy and abnormal anthers.Pollen abortion occurs between pollen maturity and flowering,indicating that premature tapetum degradation may be the primary cause of pollen abortion.Overall,our study provides a theoretical basis for utilizing CMS in hybrid breeding and in-depth investigation of the dominant configuration of cotton hybrid combinations,mechanisms of sterility,and the role of sterile and restorer genes.

An Image-Based Diagnostic Expert System for Corn Diseases

The annual worldwide yield losses due to pests are estimated to be billions of dollars. Integrated pest management （IPM） is one of the most important components of crop production in most agricultural areas of the world, and the effectiveness of crop protection depends on accurate and timely diagnosis of phytosanitary problems. Accurately identifying and treatment depends on the method which used in disease and insect pests diagnosis. Identifying plant diseases is usually difficult and requires a plant pathologist or well-trained technician to accurately describe the case. Moreover, quite a few diseases have similar symptoms making it difficult for non-experts to distinguish disease correctly. Another method of diagnosis depends on comparison of the concerned case with similar ones through one image or more of the symptoms and helps enormously in overcoming difficulties of non-experts. The old adage ＇a picture is worth a thousand words＇ is crucially relevant. Considering the user＇s capability to deal and interact with the expert system easily and clearly, a webbased diagnostic expert-system shell based on production rules （i.e., IF 〈 effects 〉 THEN 〈 causes 〉） and frames with a color image database was developed and applied to corn disease diagnosis as a case study. The expert-system shell was made on a 32-bit multimedia desktop microcomputer. The knowledge base had frames, production rules and synonym words as the result of interview and arrangement. It was desired that 80% of total frames used visual color image data to explain the meaning of observations and conclusions. Visual color image displays with the phrases of questions and answers from the expert system, enables users to identify any disease, makes the right decision, and chooses the right treatment. This may increase their level of understanding of corn disease diagnosis. The expert system can be applied to diagnosis of other plant pests or diseases by easy changes to the knowledge base.

Soil aggregation and aggregate-associated organic carbon under typical natural halophyte communities in arid saline areas of Northwest China

Information on the effects of halophyte communities on soil organic carbon(SOC)is useful for sequestrating C in arid regions.In this study,we identified four typical natural halophyte communities in the Manasi River Basin in Xinjiang Province,Northeast China,namely,Karelinia caspia(Pall.)Less.,Bassia dasyphylla(Fisch.et C.A.Mey.)Kuntze,Haloxylon ammodendron(C.A.Mey.)Bunge,and Tamarix ramosissima Lour.We compared soil aggregation and aggregated-associated SOC under these communities.The aggregate fraction of 0.053–0.25 mm accounted for 47%–75%of the total soil mass,significantly more than the>0.25 and<0.053 mm fractions,under all the halophyte communities.Significant differences in soil aggregate size distribution were observed among the plant communities,with the H.ammodendron and B.dasyphylla communities showing the highest proportions of>0.25 mm aggregates(13.3%–43.8%)and T.ramosissima community having more<0.053 mm aggregates(14.1%–27.2%).Aggregate-associated SOC concentrations were generally the highest in the>0.25 mm fraction,followed by the<0.053 mm fraction,and were the lowest in the 0.053–0.25 mm fraction;however,because of their large mass,0.25–0.053 mm aggregates contributed significantly more to the total SOC.Total SOC concentrations(0–60 cm depth)decreased in the order of H.ammodendron(5.7 g kg^-1)>T.ramosissima(4.9 g kg^-1)>K.caspia(4.2 g kg^-1)>B.dasyphylla(3.4 g kg^-1).The H.ammodendron community had the highest total SOC and aggregate-associated SOC,which was primarily because aggregate-associated SOC content at the 0–10 and 10–20 cm depths under this community were higher than those under other plant communities.The H.ammodendron community could be beneficial for increasing SOC in saline soils in the arid region.

Remote real-time monitoring soil water potential system based on GSM

Aiming at the limitation of traditional measuring soil water potential, the paper presents an information system based GSM to real-time monitor data coming from multiple data sources. The monitoring system, which consisted of monitoring center, GSM transmission channel and data detection terminal, was given. The detection terminal included the measuring station and TS-2 negative pressure meter, which was applied to measure soil water potential. Nowadays the system has been successfully applied to drip irrigation in the cotton field on farm in Xinjiang region. The system provides a feasible technology frame-work for collecting and processing wide geographical distribution data in farmland.

Studies on cDNA Probe Detection Technology for Apple Stem Pitting Virus in Kuala Pear

Using Kuala pear leaves and cortexes as materials, the total RNA was extracted using two methods and these two methods were compared. The most suited methods for Kuala pear were screened; and biotin-labeled cDNA probe was synthesized using RT-PCR. The main factors that affected the sensitivity of hybridization were studied. Studies indicated that the highest sensitivity was obtained under the following conditions： probe concentration 400 ng mL^-1, formamide concentration 45%, temperature 42℃, hybridization time 6 hours. The best hybridization results were obtained when the nitrocellulose membrane purchased from Gelman was used. Better blocking of hybridization was obtained using Tween 20 compared with albumin in bovine. The detection of the total RNA using different tissues and different extraction methods was compared. This study indicates that the total RNA of fresh leaf, old leaf, cortexes, and frozen leaf showed signs of hybridization using the two extraction methods.