Genetic Mapping And QTL Analysis Of Fiber Quality Traits Using A Three-Parent Composite Population In Upland Cotton (Gossypium Hirsutum L.)

Cotton (Gossypium spp.), one of the most economically important crops worldwide, is a renewable source of natural fiber and secondary products such as oil, livestock feed and cellulose. The genus Gossypium comprises approximately 45 diploid and 5 tetraploid species, including 4 cultivated species, G. arboreum, G. herbaceum, G. hirsutum and G. barbadense. Of the cultivated species, G. hirsutum supplies over 95% of the world's total fiber production.During the past decades, cotton breeders have placed more emphasis on increasing yield. As the basic raw materials for textile industry, fiber quality is highly correlated with spinning performance and end product quality. Technological advance in the textile industry requires high fiber quality. This requirement has attracted more efforts toward improving fiber properties, especially those of upland cotton.Conventional cultivar breeding programs, primarily relying on intermating adapted upland cotton genotypes and selecting novel allele combinations based on phenotypic selection, have certainly improved fiber quality while also increasing fiber yields in upland cotton. However, the quantitative inheritance and unfavorable correlations between lint yield and fiber quality greatly limited the efficiency of conventional breeding efforts in upland cotton improvement. Therefore, it needs to develop more effective strategies in the future cotton breeding programs.Great advances in DNA maker technologies have provided new insights on genetic improvement of cotton fiber quality. Based on the detailed molecular linkage maps, quantitative trait locus (QTL) affecting fiber quality traits could be mapped, genetically evaluated and selected through linked markers (marker-assisted selection, MAS), and even cloned (map-based cloning). Combining the powerful molecular tools and conventional breeding will provide effective approaches to select and develop cotton cultivars with improved fiber quality. Since the first molecular linkage map was constructed in cotton, genetic maps derived from interspecific populations are relatively saturated. However, so far the interspecific maps have little use in upland cotton breeding programs. The most extensive coverage map of upland cotton spanned 3,140.9 cM, accounting for 70.6% of the whole tetraploid cotton genome. Because the level of intrapecific polymorphism revealed by DNA markers is low in upland cotton, the resolution available in the existing intraspecific maps is satisfactory neither for MAS nor for map-based cloning. To obtain high-density intraspecific map, which can be used in MAS and map-based cloning in upland cotton, it needs to develop new type of markers, use upland cotton cultivars/lines with high polymorphism as mapping parents, or employ new type of mapping populations.Composite cross populations (CP), developed from three/more cultivars/parental lines, are frequently applied in crop cultivar development programs to improve agronomic and economic traits through gradually accumulating the additive effects of novel allele combinations based on phenotypic selection. However, historically linkage analysis and QTL mapping in cotton routinely capitalize on the populations derived from simple crosses (e.g., F2 and backcross). Upland cotton genetic maps in simple crosses showed limited resolution, most likely as a result of low polymorphism between two mapping parents. QTL detected in a simple cross merely represent the paucity of genetic architecture in traits, whereas a large amount of QTL information could not be exploited. Furthermore, at most two allelic effects are able to be characterized in crosses involving two inbred lines, which is a limitation to feasible options for designing optimum breeding strategies grounded on MAS. Employing CP into linkage analysis and QTL mapping may increase the marker density of upland genetic maps, exploit more adequate gene resources and facilitate MAS.In the present study, molecular markers and segregating population derived from three parents were used to develop genetic linkage map and to exploit QTL concerned with fiber quality traits. Three upland cultivars/lines, Yumianl, CRI 35 and 7235 were used to obtain the segregating population, Yumianl/CRI 35//Yumianl/7235, and its F1:2/3 inbreed lines. A linkage map developed from CP was constructed by JoinMap4.0. Based on 3 years of phenotypic data, QTL for five fiber quality traits, fiber elongation (FE), fiber length (FL), fiber micronaire reading (FM), fiber strength (FS), and fiber length uniformity ratio (FU) were analysed by MapQTL5.0. The results are followed:1. Polymorphism of SSR markers and genotypingIn total,16,052 SSR primer pairs were used to screen the polymorphism among Yumian 1, CRI 35 and 7235, and 1,057, acconting for 6.6% of the tatal primer pairs, showed effective polymorphism. The effective polymorphic primer pairs (1,057) produced 1,067 loci when they were used to genotype the CP individuals. Chi-square test showed that 375 loci significantly distorted from the expected segregation ratio (P＜0.05), accounting for 35.1% of the total loci.2. Genetic mapconstructionWhen 1,067 loci were used to construct the linkage groups, a map with 978 loci and 69 groups was obtained, remaining 89 loci unlinked.The map spanned 4,184.4 cM with an average distance of 4.3 cM between two markers, accounting for about 94.1% of the whole tetraploid cotton genome. Sixty-five of sixty-nine linkage groups were assigned to 26 chromosomes of tetraploid cotton. The remaining 4 linkage groups could not be associated with any chromosome and were tentatively named as "Un" following a number. Thirty-two linkage groups were assigned to A-subgenome, containing 366 loci, and spanning 1,954.3 cM with an average distance of 5.3 cM between two markers. Thirty-three linkage groups were assigned to D-subgenome, containing 599 loci, and spanning 2,122.1 cM with an average distance of 3.5 cM between two markers.3. Fiber quality phenotypes of mapping parents, F1 and F1:2/3familiesIn year 2007,2008 and 2009, the fiber length of 7235 were 31.9,34.5 and 34.1 mm, respectively, which was higher than that of Yumian 1 (29.9,30.3 and 30.6 mm) and CRI 35 (29.3, 30.2 and 31.4 mm). In year 2007,2008 and 2009, the parental lines, Yumian 1 and 7235, exhibited relatively higher fiber strength (38.1,34.2 and 41.3 cN/tex and 38.6,36.2 and 41.3 cN/tex) than CRI 35 (33.5,30.7 and 34.9 cN/tex). The other fiber quality traits of three parental lines were close to each other.In year 2007, fiber length ranged from 28.2 to 34.4 mm, and averaged 31.2 mm; Fiber length uniformity ranged from 80.9 to 88.1% and averaged 85.3%; Fiber strength ranged between 29.2 and 39.7 cN/tex, averaged 34.0 cN/tex; Fiber elongation was 6.5% on average and ranged from 6.2 to 6.7%; Fiber micronare reading ranged between 3.5-5.0, and averaged 4.2. In year 2008, fiber length ranged from 28.4 to 34.8 mm, and averaged 31.9 mm; Fiber length uniformity ranged from 81.6 to 87.5% and averaged 85.4%; Fiber strength ranged between 29.8 and 39.3 cN/tex, averaged 34.0 cN/tex; Fiber elongation was 6.6% on average and ranged from 6.3 to 6.8%; Fiber micronare reading ranged between 3.1-5.2 and averaged 4.1. In year 2009, fiber length ranged from 29.4 to 36.2 mm, and averaged 32.0 mm; Fiber length uniformity ranged from 82.3 to 87.4% and averaged 85.3%; Fiber strength ranged between 31.6 and 43.9 cN/tex, averaged 37.3 cN/tex; Fiber elongation was 6.6% on average and ranged from 6.3 and 6.9%; Fiber micronare reading ranged between 3.1-5.1, and averaged 4.1. Among all five fiber traits, transgressive segregation was oberserved except for fiber elongation.Singnificantly positive correlations were observered between different fiber traits except for fiber micronare reading and length, fiber micronare reading and strength, with correlation coefficients ranged from 0.276-0.687. Singnificantly negative correlations were observered between micronare reading and length, fiber micronare reading and strength, with correlation coefficients-0.472 and-0.321, respectively.The variance analysis indicated that fiber micronare reading was significantly influenced by both genotype (P＜0.01) and environment (P＜0.01); fiber length uniformity and elongation were influenced by neither genotype nor environment; fiber length was significantly influenced by environment (P＜0.05), but not by genotype; fiber strength was significantly influenced by both genotype (P＜0.05) and environment (P＜0.01). 4. QTL mapping of fiber quality traitsAll the five fiber quality traits segregated continuously and transgressive segregations were observed for fiber length, length uniformity, micronaire reading and strength. Totally,63 QTL were identified for five fiber quality traits, and mapped on 18 chromosomes and 2 Un linkage groups, including 27 significant QTL with the LOD thresholds more than the permutation-based LOD thresholds and 36 putative QTL with the LOD thresholds between 3.0 and the permutation-based LOD thresholds.For fiber elongation, nine significant QTL and two putative QTL were identified, and explained phenotypic variation between 10.5 and 47.1%. Only significant QTL qFE24.2 was detected in two environments (in year 2007 and 2008).For fiber length, sixteen QTL were identified, and explained phenotypic variation between 8.6 and 55.8%. Two significant QTL and fourteen putative QTL were detected in one environment except for putative QTL qFLunO2.1, which was detected in year 2007 and 2008.For fiber micronaire reading, six significant QTL and three putative QTL were identified, and explained phenotypic variation between 9.6 and 34.7%. Four significant QTL were detectedin two environments, and one of the four QTL. qFM03.1, was detected in year 2007 and 2008, and three others, qFM24.2, qFM24.3 and qFM24.4, were detected in year 2007 and 2009.For fiber strength, six significant QTL and four putative QTL were identified, and explained phenotypic variation between 8.1 and 32.6%. All the QTL for fiber strength were detected only in one environment.For fiber length uniformity, four significant QTL and thirteen putative QTL were identified, and explained phenotypic variation between 12.1 and 50.5%. All the QTL for fiber length uniformity were detected only in one environment.Among the QTL detected, six QTL were detected in two environments, which showed stablity in different environments. According to the sharing common markers, eleven QTL identified in the present study were also found in the same chromosome region in other populations, and these QTL included qFE24.2, qFL23.2, qFL24.2, qFM23.1, qFM24.2, qFM24.3, qFS07.1, qFS23.1, qFE24.2, qFS24.2 and qFS24.3. The QTL identified in the two environments and across different populations are of great value for MAS programs in cotton.Among the 63 QTL detected,36 and 28 alleles leading to an increase in all 5 fiber quality traits were conferred by Yumian 1 in CRI 35 and 7235 genetic background, respectively. CRI 35 contributed 23 alleles to increase five fiber quality traits.7235 contributed 33 alleles to increase fiber quality traits...