A draft physical map of a D-genome cotton species (Gossypium raimondii)

Lin, Lifeng; Pierce, Gary J.; Bowers, John E.; Estill, James C.; Compton, Rosana; Rainville, Lisa K.; Kim, Changsoo; Lemke, Cornelia; Rong, Junkang; Tang, Haibao; Wang, Xiyin; Braidotti, Michele; Chen, Amy H.; Chicola, Kristen A.; Collura, Kristi; Epps, Ethan; Golser, Wolfgang; Grover, Corrinne E.; Ingles, Jennifer; Karunakaran, Santhosh; Kudrna, Dave; Olive, Jaime; Tabassum, Nabila; Um, Eareana; Wissotski, Marina; Yu, Yeisoo; Zuccolo, Andrea; Rahman, Md Jamilur; Peterson, Daniel G.; Wing, Rod A.; Wendel, Jonathan F.; Paterson, Andrew H.

doi:10.1186/1471-2164-11-395

Cited by 47 publications

(36 citation statements)

References 89 publications

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“…The unassembled genomic regions are likely to contain heterochromatic satellites, large repetitive sequences or ribosomal RNA (rRNA) genes. Using a set of 1,369 molecular markers from a consensus genetic linkage map reported previously 17 , 43.8% of the markers (599) were unambiguously located on the assembly, allowing us to anchor 73.2% of the assembled 567.2 Mb on the G. raimondii chromosomes (Supplementary Fig. 1).…”

Section: Sequencing and Assemblymentioning

confidence: 99%

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The draft genome of a diploid cotton Gossypium raimondii

et al. 2012

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Cotton is one of the most economically important crop plants worldwide. Its fiber, commonly known as cotton lint, is the principal natural source for the textile industry. Approximately 33 million ha (5% of the world's arable land) is used for cotton planting 1 , with an annual global market value of textile mills of approximately $630.6 billion in 2011 (MarketPublishers; see URLs). Apart from its economic value, cotton is also an excellent model system for studying polyploidization, cell elongation and cell wall biosynthesis 2-5 .The Gossypium genus contains 5 tetraploid (AD 1 to AD 5 , 2n = 4×) and over 45 diploid (2n = 2×) species (where n is the number of chromosomes in the gamete of an individual), which are believed to have originated from a common ancestor approximately 5-10 million years ago 6 . Eight diploid subgenomes, designated as A to G and K, have been found across North America, Africa, Asia and Australia. The haploid genome size of diploid cottons (2n = 2× = 26) varies from about 880 Mb (G. raimondii Ulbrich) in the D genome to 2,500 Mb in the K genome 7,8 . Diploid cotton species share a common chromosome number (n = 13), and high levels of synteny or colinearity are observed among them 9-12 . The tetraploid cotton species (2n = 4× = 52), such as G. hirsutum L. and Gossypium barbadense L., are thought to have formed by an allopolyploidization event that occurred approximately 1-2 million years ago, which involved a D-genome species as the pollen-providing parent and an A-genome species as the maternal parent 13,14 . To gain insights into the cultivated polyploid genomes-how they have evolved and how their subgenomes interact-it is first necessary to have a basic knowledge of the structure of the component genomes. Therefore, we have created a draft sequence of the putative D-genome parent, G. raimondii, using DNA samples prepared from Cotton Microsatellite Database (CMD) 10 (refs. 15,16), a genetic standard originated from a single seed (accession D 5 -3) in 2004 and brought to near homozygosity by six successive generations of self-fertilization. We believe that sequencing of the G. raimondii genome will not only provide a major source of candidate genes important for the genetic improvement of cotton quality and productivity, but it may also serve as a reference for the assembly of the tetraploid G. hirsutum genome. RESULTS Sequencing and assemblyA whole-genome shotgun strategy was used to sequence and assemble the G. raimondii genome. A total of 78.7 Gb of next-generation Illumina paired-end 50-bp, 100-bp and 150-bp reads was generated by sequencing genome shotgun libraries of different fragment lengths (170 bp, 250 bp, 500 bp, 800 bp, 2 kb, 5 kb, 10 kb, 20 kb and 40 kb) that covered 103.6-fold of the 775.2-Mb assembled G. raimondii genome (Supplementary Table 1). The resulting assembly appeared to cover a very large proportion of the euchromatin of the G. raimondii genome. The unassembled genomic regions are likely to contain heterochromatic satellites, large repetitive sequences or ribosoma...

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Section: Sequencing and Assemblymentioning

confidence: 99%

“…We aligned the marker sequences from the cotton consensus map 17 to the scaffolds using blastn (identities ≥ 95%; e value ≤ 1.0 × 10 −6 ; coverage ≥ 85%), and the best-scoring match was chosen in cases of multiple matches.…”

Section: Competing Financial Interestsmentioning

confidence: 99%

The draft genome of a diploid cotton Gossypium raimondii

et al. 2012

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“…More recently, Zhang et al [15] developed a composite crossing population in upland cotton and constructed a genetic map spanned 4184.4 cm, covering approximately 94.1% of the entire tetraploid cotton genome and containing 978 simple sequence repeat (SSR) loci. A draft physical map of a D-genome cotton species (Gossypium raimondii Ulbr., D5) has been completed [16][17][18] and the G. hirsutum genome is being sequenced (http://www.monsanto.com/newsviews/Pages/Monsanto-Illumina-Key-Milestone-Cotton-Ge nome-Sequencing.aspx), which will provide rich SSR markers and functional markers for construction of high-density genetic linkage map and QTL mapping for fiber quality traits to facilitate MAS. In the present study, a high-density genetic map was constructed using an F 2 population derived from an upland cotton hybrid and used for tagging cotton fiber quality in upland cotton.…”

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Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

Liang

Hua

et al. 2013

Chin. Sci. Bull.

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With the development in spinning technology, the improvement of cotton fiber quality is becoming more and more important. The main objective of this research was to construct a high-density genetic linkage map to facilitate marker assisted selection for fiber quality traits in upland cotton (Gossypium hirsutum L.). A genetic linkage map comprising 421 loci and covering 3814.3 cM, accounting for approximately 73.35% of the cotton genome, was constructed using an F 2 population derived from cross GX1135 (P 1 )×GX100-2 (P 2 ). Forty-four of 49 linkage groups were assigned to the 26 chromosomes. Fiber quality traits were investigated in F 2 population sampled from individuals, and in F 2:3 , and F 2:4 generations sampled by lines from two sites and one respectively, and each followed a randomized complete block design with two replications. Thirty-nine quantitative trait loci were detected for five fiber quality traits with data from single environments (separate analysis each): 12 for fiber length, five for fiber uniformity, nine for fiber strength, seven for fiber elongation, and six for fiber micronaire, whereas 15 QTLs were found in combined analysis (data from means of different environments in F 2:3 generation). Among these QTLs, qFL-chr5-2 and qFL-chr14-2 for fiber length were detected simultaneously in three generations (four environments) and verified further by combined analysis, and these QTLs should be useful for marker assisted selection to improve fiber quality in upland cotton.upland cotton (Gossypium hirsutum L.), fiber quality traits, genetic linkage map, marker assisted selection, QTLs Citation:Liang Q Z, Hu C, Hua H, et al. Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.). Chin Sci Bull, 2013, 58: 32333243,

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“…The high number of informative markers obtained by highthroughput sequencing enabled genetic anchoring at a clone-by-clone scale and thereby provided an independent method of validating the physical map. This method could also complement other genome projects following a hierarchical shotgun strategy (Paux et al, 2008;Lin et al, 2010;Dohm et al, 2012). At present, POPSEQ anchoring of the barley physical map is limited by the paucity of high-quality sequence information from each individual BAC contig.…”

Section: Discussionmentioning

confidence: 99%

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

et al. 2013

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Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.

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A draft physical map of a D-genome cotton species (Gossypium raimondii)

Cited by 47 publications

References 89 publications

The draft genome of a diploid cotton Gossypium raimondii

The draft genome of a diploid cotton Gossypium raimondii

Construction of a linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

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