ATG-anchored AFLP (ATG-AFLP) analysis in cotton

Lu, Yingzhi; Curtiss, Jessica; Miranda, D.; Hughs, E.; Zhang, Jinfa

doi:10.1007/s00299-008-0568-z

Cited by 9 publications

(4 citation statements)

References 32 publications

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“…In ongoing research, these polymorphic markers were tested in a recombinant inbred line (RIL) population of 70 lines derived from a cross between NM 24016 and 3‐79. As with other markers (Lu et al, 2008), segregation of six fiber gene markers violated the expected 1:1 ratio.…”

Section: Resultsmentioning

confidence: 51%

“…These genotypes were uniform in phenotypes and were considered genetically homozygous since they were maintained by selfing. The five genotypes TM‐1, NM 24016, 3‐79, Acala 1517‐99, and PHY 76 have been used as parental lines for developing mapping populations in our laboratory (Lu et al, 2004; Zhang et al, 2005c; Lu et al, 2008; Zhang and Percy, 2008). To distinguish homologous SNP loci from homeologs in the disomic tetraploid cotton, their likely ancestral diploid species (Wendel and Cronn, 2002), G. herbaceum (A 1 –genome) and G. raimondii (D 5 –genome), were also included in this assay.…”

Section: Methodsmentioning

confidence: 99%

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DNA Polymorphisms of Genes Involved in Fiber Development in a Selected Set of Cultivated Tetraploid Cotton

Curtiss

Percy

et al. 2009

Crop Science

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The lack of genetic diversity within cultivated upland cotton (Gossypium hirsutum L.) has hindered the construction of genomewide linkage maps and their applications in genetics and breeding. The objective of this investigation was to develop candidate gene markers for fiber quality and yield on the basis of approximately 90 genes implicated in fiber development. Polymorphisms using sequence‐tagged site (STS) and single nucleotide polymorphism (SNP) markers based on single strand conformation polymorphism (SSCP) and cleaved amplified polymorphism (CAP) were evaluated among three upland and five Pima cotton (G. barbadense L.) genotypes. Of the 90 primer pairs, 75 resulted in polymerase chain reaction amplifications, including 11 that yielded polymorphic STS markers. Of the 48 primer pairs that produced polymorphic SSCP markers, 27 yielded interspecific polymorphism, while 15 yielded both inter‐ and intraspecific polymorphisms. Six pairs yielded only intraspecific polymorphisms. A total of 18 SNPs, including four indels, were identified in seven of the 15 fiber gene fragments on the basis of direct DNA sequencing, and the average length was 350 bp, with a mean of 1.3 SNPs per fragment. The average rate of SNPs per nucleotide was 0.34%, and 0.31% and 0.41% in coding and noncoding regions, respectively. Eight of the 15 SNPs were interspecific and 78% were nucleotide substitutions, with the four indels contributing to interspecific polymorphism. Six selected SNPs were confirmed by restriction enzyme digestion. The high level of SSCP polymorphism observed within a selected set of agronomically improved lines of upland cotton suggests that the use of SSCP will greatly facilitate genomewide mapping in upland cotton.

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Section: Resultsmentioning

confidence: 51%

Section: Methodsmentioning

confidence: 99%

DNA Polymorphisms of Genes Involved in Fiber Development in a Selected Set of Cultivated Tetraploid Cotton

Curtiss

Percy

et al. 2009

Crop Science

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“…The three primer pairs ( EcoR I-labelled primers) used here were designed with three base pair anchors that target specific and conserved regions within most plant genomes, similar to sequence-specific amplified polymorphisms (SSAP, [40]). The EcoR I-ATG anchor (which also has the highest PIC value of 0.196), was designed to target gene transcription initiation regions (ATG-) which are conserved motifs (AUG) found throughout the genome within coding, intronic and intergenic regions [41]. The intermediately variable of the three primers tested here (PIC = 0.184) targets the TATA-box region (TATAA-motif) upstream from the transcription initiation motif (ATG), which is a highly conserved but rare region that has been recorded in all species investigated to date [42].…”

Section: Discussionmentioning

confidence: 99%

Towards a Transferable and Cost-Effective Plant AFLP Protocol

2013

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Amplified fragment length polymorphism (AFLP) is a powerful fingerprinting technique that is widely applied in ecological and population genetic studies. However, its routine use has been limited by high costs associated with the optimization of fluorescently labelled markers, especially for individual study systems. Here we develop a low-cost AFLP protocol that can be easily transferred between distantly related plant taxa. Three fluorescently labelled EcoRI-primers with anchors that target interspecifically conserved genomic regions were used in combination with a single non-labelled primer in our AFLP protocol. The protocol was used to genotype one gymnosperm, two monocot and three eudicot plant genera representing four invasive and four native angiosperm species (Pinus pinaster (Pinaceae), Pennisetum setaceum and Poa annua (Poaceae), Lantana camara (Verbenaceae), Bassia diffusa (Chenopodiaceae), Salvia lanceolata, Salvia africana-lutea, and Salvia africana-caerulea (Lamiaceae)). Highly polymorphic and reproducible genotypic fingerprints (between 37–144 polymorphic loci per species tested) were obtained for all taxa tested. Our single protocol was easily transferred between distantly related taxa. Measures of expected heterozygosity ranged from 0.139 to 0.196 for P. annua and from 0.168 to 0.272 for L. camara which compared well with previously published reports. In addition to ease of transferability of a single AFLP protocol, our protocol reduces costs associated with commercial kits by almost half. The use of highly conserved but abundant anchor sequences reduces the need for laborious screening for usable primers that result in polymorphic fingerprints, and appears to be the main reason for ease of transferability of our protocol between distantly related taxa.

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“…DNA markers were developed to tag somatic embryogenesis (Zhang et al, 2011a), miRNA genes (Chen et al, 2013;Pang et al, 2011), a CMS cytoplasm (Suzuki et al, 2013c), male fertility restoration (Wang et al, 2007(Wang et al, , 2009Zhang and Stewart, 2004b), semigamy (Curtiss et al, 2012b), resistance gene analogs (RGA) (Hinchliffe et al, 2005;Niu et al, 2011;Zhang et al, 2007e), root-knot nematode resistance (Mi2) (Niu et al, 2007(Niu et al, , 2011, differentially expressed genes during fiber development (Li et al, 2013), and cellulose synthase genes (Lin et al, 2012). Many different marker systems have been developed, including promoter-anchored markers (PAAP-RAPD and PAAP-AFLP, Pang et al, 2009), cleaved AFLP (Zhang et al, 2005c), and other AFLPbased gene-targeted markers (GT-AFLP) including ATG-AFLP (Lu et al, 2008), TF-AFLP (Zhang et al, 2007d), miRNA-AFLP (Pang et al, 2011), PPR-AFLP (Wang et al, 2009), and RGA-AFLP (Fang et al, 2014a;Niu et al, 2011;Zhang et al, 2007e). Gene specific markers were developed for fiber genes (Lu et al, 2009) and drought responsive genes (Rodriguez-Uribe et al, 2014).…”

Section: Genomics and Molecular Breedingmentioning

confidence: 99%

History and Progress in Cotton Breeding, Genetics, and Genomics in New Mexico

Zhang¹

2018

JCS

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The New Mexico Cotton Breeding Program was established in 1926 and has been led by five generations of breeders. The program has released 37 Acala 1517 and one short-staple Upland cotton (Gossypium hirsutum L.) cultivars and numerous germplasm lines. Two Sea-Island G. barbadense L. cultivars have been released for production in the Mesilla Valley, NM. New Mexico germplasm has contributed to the development of 45% of the commercial cotton cultivars including almost all Acala cultivars in California, and has contributed to the improvement in fiber length and strength in U.S. cottons. Many Acala 1517 cultivars are tolerant or resistant to Verticillium wilt and bacterial blight. The recent releases include three transgenic Acala 1517 cultivars, one conventional and two glandless cultivars. The current research program focuses on fiber and seed quality (glandless) to develop elite germplasm with high yields and superior fiber quality and with resistance to Verticillium and Fusarium wilt, thrips, bacterial blight, leaf spot, cotton rust, and tolerance to drought and salinity. Upland × Pima introgression and development of the hybrid seed production system based on cytoplasmic male sterility and the haploid-producing system based on semigamy are also important aspects of the program. Extensive applications of genomic tools and approaches in the program include DNA marker and population development, linkage map construction, and quantitative trait locus mapping. In recent years, reduction in funding and lack of institutional support has hampered the program in delivering solutions to challenging issues such as Fusarium wilt race 4 faced by the cotton farmer.

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ATG-anchored AFLP (ATG-AFLP) analysis in cotton

Cited by 9 publications

References 32 publications

DNA Polymorphisms of Genes Involved in Fiber Development in a Selected Set of Cultivated Tetraploid Cotton

DNA Polymorphisms of Genes Involved in Fiber Development in a Selected Set of Cultivated Tetraploid Cotton

Towards a Transferable and Cost-Effective Plant AFLP Protocol

History and Progress in Cotton Breeding, Genetics, and Genomics in New Mexico

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