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Agronomy
Special Issues
Cotton Breeding, Genetics and Genomics
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Cotton Breeding, Genetics and Genomics

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (28 February 2019) | Viewed by 17145

Special Issue Editor

Dr. Qian-Hao Zhu

E-Mail Website
Guest Editor
CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
Interests: cotton biology; genomics; molecular breeding; plant noncoding RNAs; biostress tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Releasing of the Gossypium raimondii and G. hirsutum genome sequences provided valuable genomic resources for the most important cash crop—cotton. Together with the next-generation sequencing and high-throughput genotyping technologies, these genomic resources have dramatically changed the way we do science in cotton, significantly promoted researches on cotton molecular genetics and functional genomics, and increased our knowledge and understanding of cotton biology. A combinational approach using multiple omics platforms and integration of their outcomes provide tools for improving the productivity of cotton through molecular breeding, such as marker-assisted selection and genomic selection.

This Special Issue would publish reviews and original research articles on the topics related to but not limited to cotton genetic analysis, transcriptomics, comparative genomics, functional genomics and molecular breeding with aims to facilitate communication among cotton scientists working on breeding, genetics and genomics and to enhance implementation of findings of genetics and genomics in breeding practices.

Dr. Qian-Hao Zhu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cotton
  • breeding
  • genomics
  • mapping-by-sequencing
  • marker-assisted selection
  • genome-wide association analysis
  • genomic selection
  • non-coding RNAs

Published Papers (4 papers)

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Research

22 pages, 432 KiB  
Article
Response of Boll Development to Macronutrients Application in Different Cotton Genotypes
by Irshad Ahmad, Guisheng Zhou, Guanglong Zhu, Zahoor Ahmad, Xudong Song, Yousaf Jamal, Muhi Eldeen Hussien Ibrahim and Nimir Eltyb Ahmed Nimir
Agronomy 2019, 9(6), 322; https://doi.org/10.3390/agronomy9060322 - 19 Jun 2019
Cited by 8 | Viewed by 3119
Abstract
Combined application of nitrogen (N), phosphorus (P), and potassium (K) is a valuable practice to improve the growth and physiological activities of cotton, especially during a boll setting. The main purpose of this research was to investigate the effects of the different combined [...] Read more.
Combined application of nitrogen (N), phosphorus (P), and potassium (K) is a valuable practice to improve the growth and physiological activities of cotton, especially during a boll setting. The main purpose of this research was to investigate the effects of the different combined ratios of nitrogen (N), phosphorus (P), and K (potassium) on morpho-physiological activities of Bacillus thuringiensis (Bt) cotton genotypes Siza 1 and Sikang 1 during the cotton boll development stage. A two-year (2016–2017) field experiment was performed in which the total amount of combined N, P, and K were applied at different levels, B1 = 150 N, 0 P2O5, and 0 K2O kg ha−1 (control), B2 = 150 N, 45 P2O5, and 90 K2O kg ha−1, B3 = 150 N, 90 P2O5, and 135 K2O kg ha−1, and B4 = 150 N, 135 P2O5, and 180 K2O kg ha−1. Results revealed that combined application of N, P, and K significantly increased boll length by 5.8% and 2.3%, fresh boll weight by 12.2% and 16.4%, dry lint weight by 15.2% and 1.7%, number of seeds boll−1 by 15.2% and 2.5% as well as dry boll shell weight by 11.0% and 4.9% as compared with the treatment without P and K (1:0:0) across two growing seasons. Furthermore, superoxide dismutase activity was improved by 2.3% and 15.6% and soluble protein by 5.1% and 14.1% as compared with the control, respectively. Our study indicated that combined application of N, P, and K at appropriate ratios enhanced morpho-physiological activities (boll length, boll width, boll weight, protein content, sugar content, and superoxide dismutase) of cotton during boll development and generally the ratio of 150:135:180 considerably performed best amongst all treatments during two growing seasons in this study. Full article
(This article belongs to the Special Issue Cotton Breeding, Genetics and Genomics)
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16 pages, 2535 KiB  
Article
Genome Resequencing Reveals Genetic Variation between the Parents of An Elite Hybrid Upland Cotton
by Chengxiang Song, Wei Li, Zhenyu Wang, Xiaoyu Pei, Yangai Liu, Zhongying Ren, Kunlun He, Fei Zhang, Kuan Sun, Xiaojian Zhou, Xiongfeng Ma and Daigang Yang
Agronomy 2018, 8(12), 305; https://doi.org/10.3390/agronomy8120305 - 17 Dec 2018
Cited by 7 | Viewed by 3881
Abstract
Cotton is one of the most important economic crops worldwide. As the global demands rising, cotton yield improvement is the most important goal of cotton breeding. Hybrids have great potential for increasing yield, however, the genetic mechanism of hybrids is still not clear. [...] Read more.
Cotton is one of the most important economic crops worldwide. As the global demands rising, cotton yield improvement is the most important goal of cotton breeding. Hybrids have great potential for increasing yield, however, the genetic mechanism of hybrids is still not clear. To investigate the genetic basis of cotton hybrids, we resequenced 9053 and sGK9708 with 62.13x coverage depth, the parents of the elite hybrid cotton CCRI63 that has obvious heterosis in lint percentage (LP) and boll weight (BW). Based on the cotton reference genome (TM-1), 1,287,661 single nucleotide polymorphisms (SNPs) and 152,479 insertions/deletions (InDels) were identified in 9053, and 1,482,784 SNPs and 152,985 InDels in sGK9708. Among them, 8649 SNPs and 629 InDels in the gene coding regions showed polymorphism between parents. Moreover, these variations involved 5092 genes, and 3835 of these genes were divided into 10 clusters based on the gene expression profiles. The genes in Cluster 3 and 7 were specifically expressed in the ovule and fiber development stage, suggesting that they might relate to LP and BW. We further co-localized the polymorphic SNPs and InDels with the reported quantitative trait loci (QTLs) of LP and BW, and identified 68 genes containing the polymorphic SNPs or InDels within these QTL intervals and as being related to fiber development. This suggested that the outstanding traits of CCRI63 such as LP and BW might be generated by accumulating the favorable variations from the parents. The results generated herein provide a genetic basis for cotton hybrids and genetic markers for marker-assisted selection breeding of cotton. Full article
(This article belongs to the Special Issue Cotton Breeding, Genetics and Genomics)
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13 pages, 3181 KiB  
Article
Genome-Wide Identification and Expression Analysis of the Dof Transcription Factor Gene Family in Gossypium hirsutum L.
by Huaizhu Li, Lingling Dou, Wei Li, Ping Wang, Qin Zhao, Ruimin Xi, Xiaoyu Pei, Yangai Liu and Zhongying Ren
Agronomy 2018, 8(9), 186; https://doi.org/10.3390/agronomy8090186 - 13 Sep 2018
Cited by 10 | Viewed by 4331
Abstract
Gossypium hirsutum L. is a worldwide economical crop; however, premature leaf senescence reduces its production and quality which is regulated by stresses, hormones, and genes. DNA binding with the one zinc finger (Dof) transcription factors (TFs) participate widely in plant development and responses [...] Read more.
Gossypium hirsutum L. is a worldwide economical crop; however, premature leaf senescence reduces its production and quality which is regulated by stresses, hormones, and genes. DNA binding with the one zinc finger (Dof) transcription factors (TFs) participate widely in plant development and responses to biotic and abiotic stresses, but there have been few reports of these TFs in cotton. Here, we perform a genome-wide study of G. Hirsutum L. Dof (GhDof) genes and analyze their phylogeny, duplication, and expression. In total, 114 GhDof genes have been identified and classified into nine subgroups (A, B1, B2.2, B2.1, C1, C2.1, C2.2, D1, and D2) based on phylogenetic analysis. An MCScanX analysis showed that the GhDof genes expanded due to segmental duplications. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that GhDofD9.6 was not only differentially expressed between CCRI10 (with premature senescence) and Liao4086 (without premature senescence) but also responded to salinity stress; GhDofA5.7, GhDofA7.4, GhDofA8.2, GhDof11.1, GhDofD7.2, and GhDofD11.3 signfificantly responded to cold (4 °C) stress. This work lays the foundation for further analysis of the function of GhDof genes in G. hirsutum, which will be helpful for improving the production and quality of cotton. Full article
(This article belongs to the Special Issue Cotton Breeding, Genetics and Genomics)
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15 pages, 4371 KiB  
Article
Genome-Wide Mining and Characterization of SSR Markers for Gene Mapping and Gene Diversity in Gossypium barbadense L. and Gossypium darwinii G. Watt Accessions
by Allah Ditta, Zhongli Zhou, Xiaoyan Cai, Muhammad Shehzad, Xingxing Wang, Kiflom Weldu Okubazghi, Yanchao Xu, Yuqing Hou, Muhammad Sajid Iqbal, Muhammad Kashif Riaz Khan, Kunbo Wang and Fang Liu
Agronomy 2018, 8(9), 181; https://doi.org/10.3390/agronomy8090181 - 12 Sep 2018
Cited by 7 | Viewed by 5115
Abstract
The present study aimed to characterize the simple sequence repeat markers in cotton using the cotton expressed sequence tags. A total of 111 EST-SSR polymorphic molecular markers with trinucleotide motifs were used to evaluate the 79 accessions of Gossypium L., (G. darwinii [...] Read more.
The present study aimed to characterize the simple sequence repeat markers in cotton using the cotton expressed sequence tags. A total of 111 EST-SSR polymorphic molecular markers with trinucleotide motifs were used to evaluate the 79 accessions of Gossypium L., (G. darwinii, 59 and G. barbadense, 20) collected from the Galapagos Islands. The allele number ranged from one to seven, with an average value of 2.85 alleles per locus, while polymorphism information content values varied from 0.008 to 0.995, with an average of 0.520. The discrimination power ranks high for the majority of the SSRs, with an average value of 0.98. Among 111 pairs of EST-SSRs and gSSRs, a total of 49 markers, comprising nine DPLs, one each of MonCGR, MUCS0064, and NAU1028, and 37 SWUs (D-genome), were found to be the best matched hits, similar to the 155 genes identified by BLASTx in the reference genome of G. barbadense, G. arboreum L., and G. raimondii Ulbr. Related genes GOBAR_DD21902, GOBAR_DD15579, GOBAR_DD27526, and GOBAR_AA04676 revealed highly significant expression 10, 15, 18, 21, and 28 days post-anthesis of fiber development. The identified EST-SSR and gSSR markers can be effectively used for mapping functional genes of segregating cotton populations, QTL identification, and marker-assisted selection in cotton breeding programs. Full article
(This article belongs to the Special Issue Cotton Breeding, Genetics and Genomics)
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