New ICGI co-chairs have been elected

International Cotton Genome Initiative (ICGI) has completed 2015 election process, and as a result, six new co-chairs for overall chairing and ICGI work groups have been elected for 2017-2019 terms:

ICGI Overall – Dr. John Yu (USA)

Breeding and Applied Genomics – Dr. Jodi Scheffler (USA)

Comparative Genomics and Bioinformatics – Dr. Ibrokhim Abdurakhmonov (Uzbekistan)

Functional Genomics – Dr. Guoli Song ( China)

Germplasm & Genetic Stocks – Dr. Xiongming Du (China)

Structural Genomics – Dr. Wangzhen Guo (China)

Moreover, per election results, 95-97% voters approved new Workgroup structure of ICGI and uses of ICGI funds.

Congratulations for successful election process to ICGI and its new co-chairs!

Details of ICGI election results can be fount at:

Cotton Research enters to a period of “golden” opportunities

With the recent completion of draft sequencing of diploid cotton Gossypium raimondii and G. arboreum genomes published in Nature Genetics, and the first “gold-standard” version of G. raimondii genome published in Nature, cotton research community enjoyed the pick of many seminal research results that have provided a glorious opportunity to study orthologous and paralogous genes and gene families in allotetraploid cotton.

These successes and great achievements in ancestral diploid genome sequencing further resulted in decoding of the representative genome of widely grown allotetraploid Upland (G. hirsutum L.) cotton, Texas Marker-1.

Two independent research papers published in Nature Biotechnology by Zhang et al. and Li et al. in this week issue described the complex allotetraploid TM-1 genome that further entered cotton research to an era of “golden” opportunities providing the first insights into allotetraploid cotton genome structure, genome rearrangements, gene evolution, cotton fiber biology and biotechnology that will help to rapidly translate the genomics “knowledge” to an “economic impact”!

Congratulation to all cotton community with these latest achievements, high impact journal seminal publications, and hard work to foster cotton research!

Correlation analysis of stem hardness traits with fiber and yield-related traits in core collections of Gossypium hirsutum

[BackgroundStem hardness is one of the major influencing factors for plant architecture in upland cotton (Gossypium hirsutum L.). Evaluating hardness phenotypic traits is very important for the selection of elite lines for resistance to lodging in Gossypium hirsutum L. Cotton breeders are interested in using diverse genotypes to enhance fiber quality and high-yield. Few pieces of research for hardness and its relationship with fiber quality and yield were found. This study was designed to find the relationship of stem hardness traits with fiber quality and yield contributing traits of upland cotton.

[Results] Experiments were carried out to measure the bending, acupuncture, and compression properties of the stem from a collection of upland cotton genotypes, comprising 237 accessions. The results showed that the genotypic difference in stem hardness was highly significant among the genotypes, and the stem hardness traits (BL, BU, AL, AU, CL, and CU) have a positive association with fiber quality traits and yield-related traits. Statistical analyses of the results showed that in descriptive statistics result bending (BL, BU) has a maximum coefficient of variance, but fiber length and fiber strength have less coefficient of variance among the genotypes. Principal component analysis (PCA) trimmed quantitative characters into nine principal components. The first nine principal components (PC) with Eigenvalues > 1 explained 86% of the variation among 237 accessions of cotton. Both 2017 and 2018, PCA results indicated that BL, BU, FL, FE, and LI contributed to their variability in PC1, and BU, AU, CU, FD, LP, and FWPB have shown their variability in PC2.

[Conclusion] We describe here the systematic study of the mechanism involved in the regulation of enhancing fiber quality and yield by stem bending strength, acupuncture, and compression properties of G. hirsutum.

[Title] Correlation analysis of stem hardness traits with fiber and yield-related traits in core collections of Gossypium hirsutum

[Authors] RAZA Irum, HU Daowu, AHMAD Adeel, LI Hongge, HE Shoupu, NAZIR Mian Faisal, WANG Xiaoyang, JIA Yinhua, PAN Zhaoe, ZHANG Peng, YASIR Muhammad, IQBAL Muhammad Shahid, GENG Xiaoli, WANG Liru, PANG Baoyin and DU Xiongming

Journal of Cotton Research 2021, 48

Identification, characterization, and expression profiles of the GASA genes in cotton

[Background] GASA (Giberellic Acid Stimulated in Arabidopsis) gene family plays a crucial role in the phytohormone signaling pathway, growth and development, and stress responses in plants. Many GASA homologs have been identified in various plants. Nevertheless, little is known about these proteins in cotton.

[Results] In the current study, we identified 19, 17, 25, 33, and 38 GASA genes via genome-wide analyses of Gossypium herbaceumG. arboreum, G. raimondiiG. barbadense, and G. hirsutum, respectively, and performed comprehensive bioinformatics and expression analyses. According to our results, 132 GASA proteins shared similar protein structures and were classified into four groups based on the phylogenetic tree. A synteny analysis suggested that segmental duplication was a key driver in the expansion of the GASA gene family. Meanwhile, the cis-element and protein interaction analyses indicated that GhGASA proteins play a significant role in the hormone responses. Transcriptomic and qRT-PCR (Quantitative real time-polymerase chain reaction) analyses revealed diverse expression profiles of the GhGASA genes in different organs under abiotic stresses, indicating that some GhGASA genes possibly participate in fiber development and abiotic-stress responses.

[Conclusion] The GASA genes in cotton were systematically identified and analyzed for the first time in this paper, and it suggested that the GASA genes are important to the development and growth of cotton. These results will support future exploration of the functions of GASA genes in cotton.

[Title] Identification, characterization, and expression profiles of the GASA genes in cotton

[Authors] QIAO Kaikai, MA Changkai, LV Jiaoyan, ZHANG Chaojun, MA Qifeng and FAN Shuli

Journal of Cotton Research 2021, 47

Insights into wing dimorphism in worldwide agricultural pest and host-alternating aphid Aphis gossypii

[Background] The worldwide pest Aphis gossypii has three-winged morphs in its life cycle, namely, winged parthenogenetic female (WPF), winged gynopara (GP), and winged male, which are all produced by a wingless parthenogenetic female (WLPF). Most studies on A. gossypii have focused on WPF, while few have investigated GP and male. The shared molecular mechanism underlying the wing differentiation in the three wing morphs of A. gossypii remains unknown. The wing differentiation of WPF was explored in a previous study. Herein, GP and male were induced indoors. The characters of the body, internal genitals, wing veins, and fecundity of GP and male were compared with those of WPF or WLPF. Compared with WLPF, the shared and separate differentially expressed genes (DEGs) were identified in these three-wing morphs.

[Results] Newly-born nymphs reared in short photoperiod condition (8 L:16D, 18 °C) exclusively produced gynoparae (GPe) and males in adulthood successively, in which the sex ratio was GP biased. A total of 14 GPe and 9 males were produced by one mother aphid. Compared with WLPF, the three-wing morphs exhibited similar morphology and wing vein patterns but were obviously discriminated in the length of fore- and underwings, reproductive system, and fecundity. A total of 37 090 annotated unigenes were obtained from libraries constructed using the four morphs via RNA sequencing (RNA-Seq). In addition, 10 867 and 19 334 DEGs were identified in the pairwise comparison of GP versus WLPF and male versus WLPF, respectively. Compared with WLPF, the winged morphs demonstrated 2 335 shared DEGs (1 658 upregulated and 677 downregulated). The 1 658 shared upregulated DEGs were enriched in multiple signaling pathways, including insulin, FoxO, MAPK, starch and sucrose metabolism, fatty acid biosynthesis, and degradation, suggesting their key roles in the regulation of wing plasticity in the cotton aphid. Forty-four genes that spanned the range of differential expression were chosen to validate statistical analysis based on RNA-Seq through the reverse transcription quantitative real time polymerase chain reaction (RT-qPCR). The comparison concurred with the expression pattern (either up- or downregulated) and supported the accuracy and reliability of RNA-Seq. Finally, the potential roles of DEGs related to the insulin signaling pathway in wing dimorphism were discussed in the cotton aphid.

[Conclusion] The present study established an efficiently standardized protocol for GP and male induction in cotton aphid by transferring newly-born nymphs to short photoperiod conditions (8 L:16D, 18 °C). The external morphological characters, especially wing vein patterns, were similar among WPFs, GPe, and males. However, their reproductive organs were strikingly different. Compared with WLPF, shared (2 335) and exclusively (1 470 in WLPF, 2 419 in GP, 10 774 male) expressed genes were identified in the three-wing morphs through RNA-Seq, and several signaling pathways that are potentially involved in their wing differentiation were obtained, including insulin signaling, starch and sucrose metabolism.

[Title] Insights into wing dimorphism in worldwide agricultural pest and host-alternating aphid Aphis gossypii

[Authors] JI Jichao, HUANGFU Ningbo, LUO Junyu, GAO Xueke, NIU Lin, ZHANG Shuai & CUI Jinjie

Journal of Cotton Research 2021, 45

Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

[Background] Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites.

[Results] In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes.

[Conclusion] Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

[Title]Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

[Authors] DOU Lingling, LV Limin, KANG Yangyang, TIAN Ruijie, HUANG Deqing, LI Jiayin, LI Siyi, LIU Fengping, CAO Lingyan, JIN Yuhua, LIU Yang, LI Huaizhu, WANG Wenbo, PANG Chaoyou, SHANG Haihong, ZOU Changsong, SONG Guoli & XIAO Guanghui

Journal of Cotton Research 2021, 44

QTL mapping of agronomic and economic traits for four F2 populations of upland cotton

[Background] Upland cotton (Gossypium hirsutum) accounts for more than 90% of the annual world cotton output because of its high yield potential. However, yield and fiber quality traits often show negative correlations. We constructed four F2 populations of upland cotton, using two normal lines (4133B and SGK9708) with high yield potential but moderate fiber quality and two introgression lines (Suyuan04–3 and J02–247) with superior fiber quality, and used them to investigate the genetic basis underlying complex traits such as yield and fiber quality in upland cotton. We also phenotyped eight agronomic and economic traits and mapped quantitative trait loci (QTLs).

[Results] Extensive phenotype variations and transgressive segregation were found across the segregation populations. We constructed four genetic maps of 585.97 centiMorgan (cM), 752.45 cM, 752.45 cM, and 1 163.66 cM, one for each of the four F2 populations. Fifty QTLs were identified across the four populations (7 for plant height, 27 for fiber quality and 16 for yield). The same QTLs were identified in different populations, including qBW4 and qBW2, which were linked to a common simple sequence repeat (SSR) marker, NAU1255. A QTL cluster containing eight QTLs for six different traits was characterized on linkage group 9 of the 4133B × Suyuan04–3 population.

[Conclusion] These findings will provide insights into the genetic basis of simultaneous improvement of yield and fiber quality in upland cotton breeding.

[Title] QTL mapping of agronomic and economic traits for four F2 populations of upland cotton

[Authors] LI Hongge, PAN Zhaoe, HE Shoupu, JIA Yinhua, GENG Xiaoli, CHEN Baojun, WANG Liru, PANG Baoyin & DU Xiongming

Journal of Cotton Research 2021, 43

Effects of irrigation and planting geometry on cotton (Gossypium hirsutum L.) fiber quality and seed composition

[Background] Cotton fiber quality and seed composition play vital roles in the economics of cotton production systems and the cottonseed meal industry. This research aimed to examine the effects of different irrigation levels and planting geometries on fiber quality and seed composition of cotton (Gossypium hirsutum L.). We conducted a 2-year study in 2018 and 2019 in a warm, humid area in the Southeast United States on Dundee silt loam soil. There were three irrigation treatments in the study. The treatments included irrigating every furrow, or full irrigation (FI), every alternate furrow, or half irrigation (HI), and no irrigation, or rain-fed (RF). Planting geometries were on ridges spaced 102 cm apart and either a single-row (SR) or twin-rows (TR).

[Results] The results of high-volume instrument (HVI), advanced fiber information systems (AFIS) and near-infrared reflectance spectroscopy (NIRS) showed that irrigation and planting treatments played a significant role in fiber quality and seed composition. Across irrigation treatments, significant differences were seen in fiber properties, including fineness, maturity ratio, micronaire, neps, short fiber, strength, uniformity, upper half mean length (UHML), upper quartile length by weight (UQLw), and yellowness (+b). Irrigation and planting geometry (PG) had a significant effect on micronaire, strength, and UHML while their interaction was significant only for micronaire. The micronaire was negatively affected by irrigation as FI-SR, FI-TR, HI-SR, and HI-TR recorded 11% ~ 12% lower over the RF-SR and TR treatments. The PG played a minor role in determining fiber quality traits like micronaire and nep count. Irrigation treatments produced significantly lower (3% ~ 4%) protein content than rain-fed, while oil content increased significantly (6% ~ 10%).

[Conclusion] The study results indicate a potential for improving cotton fiber and seed qualities by managing irrigation and planting geometries in cotton production systems in the Mississippi (MS) Delta region. The HI-TR system appears promising for lint and seed quality.

[Title] Effects of irrigation and planting geometry on cotton (Gossypium hirsutum L.) fiber quality and seed composition

[Authors]  PINNAMANENI Srinivasa R., ANAPALLI Saseendran S., SUI Ruixiu, BELLALOUI Nacer & REDDY Krishna N. 

Journal of Cotton Research 2021, 42