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Construction of Microsatellite-Based Linkage Map and Mapping of Nectarilessness and Hairiness Genes in Gossypium Tomentosum

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Construction of Microsatellite-Based Linkage Map and Mapping of Nectarilessness and Hairiness Genes in Gossypium Tomentosum c Indian Academy of Sciences RESEARCH ARTICLE Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum MEIYING HOU, CAIPING CAI, SHUWEN ZHANG, WANGZHEN GUO, TIANZHEN ZHANG and BAOLIANG ZHOU∗ State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China Abstract Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat, SSR)-based genetic map was constructed using the interspecific cross of G. hirsutum × G. tomentosum (HT). We detected 1800 loci from 1347 pairs of polymorphic primers. Of these, 1204 loci were grouped into 35 linkage groups at LOD ≥ 4. The map covers 3320.8 cM, with a mean density of 2.76 cM per locus. We detected 420 common loci (186 in the At subgenome and 234 in Dt) between the HT map and the map of TM-1 (G. hirsutum) and Hai 7124 (G. barbadense; HB map). The linkage groups were assigned chromosome numbers based on location of common loci and the HB map as reference. A comparison of common markers revealed that no significant chromosomal rearrangement exist between G. tomentosum and G. barbadense. Interestingly, however, we detected numerous (33.7%) segregation loci deviating from 3:1 ratio (P < 0.05) in HT, mostly clustering on eight chromosomes in the Dt subgenome, with some on three chromosomes in At. Two morphological traits, leaf hairiness and leaf nectarilessness were mapped on chromosomes 6 (A6) and 26 (D12), respectively. The SSR-based map constructed in this study will be useful for further genetic studies on cotton breeding, including mapping loci controlling quantitative traits associated with fiber quality, stress tolerance and developing chromosome segment specific introgression lines from G. tomentosum into G. hirsutum using marker-assisted selection. [Hou M., Cai C., Zhang S., Guo W., Zhang T. and Zhou B. 2013 Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum. J. Genet. 92, 445–459] Introduction leaves and stems but no nectary on its leaves or bracteoles, but has an extra floral nectary that attracts pests (Hutchinson Cotton (Gossypium spp.) is one of the world’s most impor- et al. 1947). It also has strong fibers (Meyer and Meredith tant economic crops, with world-wide cotton production 1978) and is the most heat-tolerant species of Gossypium. valued at approximately US$27–29 billion annually in 2005– These traits from G. tomentosum can be introgressed into 2007 (Campbell et al. 2010). Gossypium hirsutum L. and G. hirsutum by wide-crossing and are important for cotton G. barbadense L., which are commercially important cul- breeding. However, it is quite difficult to transfer these traits tivated species belonging to the (AD)1 and (AD)2 genome directly into cultivated cotton by conventional breeding due groups, respectively, are very susceptible to insect pests such to segregation distortion (Jiang et al. 2000), suppression as white flies, aphids, jassids and bollworms. G. tomento- of recombination (Paterson et al. 1990) and linkage drag sum Nutt ex Seem, a wild tetraploid species with (AD)3 (Young and Tanksley 1989). genome, is closely related to G. hirsutum but quite differ- Constructing a molecular map provides the foundation for ent from the tetraploid cultivated species G. hirsutum and the genetic dissection of important traits and will facilitate G. barbadense in terms of phenotype, isozymes and markers utilization of G. tomentosum in breeding by marker-assisted (Fryxell 1979; Saha and Zipf 1997). G. tomentosum has hairy selection (MAS) and map-based cloning. To date, several high density genetic molecular maps have been constructed using diverse DNA molecular markers and mapping popu- ∗ For correspondence. E-mail: [email protected]. lations (Ulloa et al. 2002; Nguyen et al. 2004; Rong et al. Keywords. microsatellite; leaf hairiness; leaf nectarilessness; genetic linkage map; Gossypium tomentosum. Journal of Genetics, Vol. 92, No. 3, December 2013 445 Meiying Hou et al. 2004;Guoet al. 2007; Zhang et al. 2009, 2012;Yuet al. G. tomentosum Nutt ex Seem grown under field conditions at 2011), but most of these are HB maps (from a cross between Jiangpu Experiment Station of Nanjing Agricultural Univer- G. hirsutum L. and G. barbadense L.). sity (NAU), China. The former is an upland cotton cultivar To date, only one HT map (from a cross between G. with high yield and moderate fiber quality, whereas the latter, hirsutum and G. tomentosum) has been reported (Waghmare a wild tetraploid species, possesses many desirable traits, et al. 2005). Using this map, Zhang et al.(2011) identified such as morphological resistance to insect pest (heavy leaf 28 QTLs controlling fiber quality traits. However, this HT hairs and nectariless leaves), heat and drought tolerance and map is difficult to use for high throughput cotton breeding good fiber quality. because the markers used in the map are hybridization-based Total genomic DNA was extracted from young leaves of (i.e., restriction fragment length polymorphism, RFLPs). the two parents, F1 and each F2 individual as described by RFLP analysis is inefficient due to large amount of high- Paterson et al.(1993) with some modifications. quality DNA required for this time-consuming process. In recent years, many new sets of molecular markers have been generated to facilitate the development of a high-resolution SSR analysis, PCR amplification and electrophoresis integrated genetic map of cotton. Among the different types of molecular markers, microsatellites or simple sequence A total of 8488 SSR primer pairs were evaluated for repeats (SSRs) are becoming the markers of choice for tag- detecting polymorphism between the two parents. All SSR ging genes and assessing genetic diversity. This is mainly primer information used in this study can be obtained from // because SSR analysis requires only a small amount of DNA. http: www.cottonmarker.org. SSR-PCR amplifications were Moreover, SSRs are easily detectable by PCR, amenable performed using a Peltier Thermal Cycler-EDC-810 (Eastwin, to high-throughput analysis, codominantly inherited, multi- Hongkong) and electrophoresis of the products was per- allelic, highly polymorphic, abundant and evenly distributed formed as described by Zhang et al.(2000, 2002). in the genome. SSRs exist throughout the entire genome of an organism in both noncoding and coding regions. These traits allow the complexity of the multilocus SSR fingerprint Phenotypic analysis to be customized; SSRs are therefore ideal for the analysis of Plants were scored for each of the following traits: F2 indi- large genomes. The unique mechanism responsible for gen- viduals were investigated for leaf pubescence and nectaries; erating SSR allelic diversity arose through replication slip- trichomes on the surface of leaves were scored as smooth page. The codominant nature of SSR markers also permits (very similar to the maternal parent, G. hirsutum L. acc the detection of a large number of alleles per locus and con- 08N2162) or heavy hairy leaves (very similar to the paternal tributes to higher levels of expected heterozygosity. Manosh parent, G. tomentosum); nectaries on the abaxial midribs of et al.(2011) found that SSRs generate the highest per- leaves were scored as present or absent. centage of mappable loci among the techniques examined, indicating that SSR markers are more suitable for mapping in citrus. Genotyping and testing for segregation distortion To effectively transfer desirable genes conferring strong fibers and high heat tolerance, entirely PCR-based linkage All 8488 SSR primer pairs were first used to screen polymor- mapping of the cross between G. hirsutum and G. tomen- phisms between the two parents. Markers found to be poly- tosum is a prerequisite for its utilization in cotton breeding. morphic were then used to survey 93 individuals of the F2 In this study, we produced and reported the first SSR mapping population. All distinctive and unambiguous poly- (PCR-based) genetic map (HT) covering a large region morphic bands were scored as 1 (present) or 0 (absent). of the cotton genome and compared with the HB map Missing data were noted as ‘–’. Each marker system identi- (constructed by Dr Zhang’s group of Nanjing Agricultural fied both monomorphic and polymorphic markers. At each University, Guo et al. 2007). Moreover, the genes conferring locus, the allele from G. hirsutum was denoted as A, whereas leaf trichome and leaf nectary were mapped as discrete mark- the allele from G. tomentosum was denoted as B. The ers. The results of this study will contribute to the alignment expected allelic ratio for F2 was 1:1 (A:B). The expected of morphological and molecular maps identification of DNA genotypic ratio was 1:2:1 (AA:AB:BB) for codominant markers diagnostic of phenotypic variation for these traits markers or 3 : 1 (dominant : recessive) for dominant markers and also improve insect resistance in cotton. in the F2 population. The observed ratios for each marker were tested for deviation from the expected values with a χ 2 goodness-of-fit test (P < 0.05). A region with at least three Materials and methods adjacent loci showing significant segregation distortion was defined as the segregation distorted region (SDR) (Paillard Plant materials and DNA extraction et al. 2003). Ninety-three individuals of the F2 generation were derived A chi-square test was used to compute segregation distor- from a single cross between G. hirsutum L. acc 08N2162 and tion by bi-parent genotypes to ascertain whether they skewed 446 Journal of Genetics, Vol. 92, No. 3, December 2013 Genetic mapping of a cross between G. hirsutum and G. tomentosum towards the female genotype or male genotype. For codom- function (Kosambi 1944) was used to convert recombina- inant markers, allele frequency (p = q) and the distribu- tion frequency to genetic map distance (centimorgen, cM).
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