Association mapping for seed cotton yield,yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes

Association mapping has revolutionized human genetics and is increasingly used in plant genetics. It is an efficient way of determining the genetic basis of complex traits. In cotton so far numerous association mapping studies are available as compared to many other important crops. In our study, mapping was performed using cotton 63K infinium beadchip with 201 germplasm lines. Through fast STRUCTURE analysis, lines were grouped into 12 subgroups and revealed genome sharing among the groups. The critical value (R²) was set to 0.243 as threshold to claim LD between two loci. About 3.13% marker pairs recorded significantly high LD (R² = 1), and 8.19% of marker pairs were in the range of 0.3 to 0.99 R². In MLM, 349 significant marker–trait associations were detected as against 642 in GLM because of effectiveness in eliminating false associations in MLM. A total of 68 markers explained >10% phenotypic variation for yield and fibre quality traits. Phenotypic variation explained by markers was smaller, suggesting that they might be associated with minor QTLs.     

Comparative efficiency of honeycomb and conventional pedigree methods of selection for yield and fiber quality in cotton (Gossypium spp.)

The effectiveness of honeycomb pedigree selection (HPS) as compared to conventional pedigree selection (CPS) was studied in one intraspecific (G. hirsutum L. × G. hirsutum L.) cross population (population I) and one interspecific (G. hirsutum L. × G. barbadense L.) cross population (population II). Combined selection for yield and lint quality traits was applied for four cycles at two locations for population I and atone location for population II. Finally, the best F₆ lines derived by each method, together with the unselected population derived by single seed descent (SSD) and three check cultivars, were tested in comparative experiments, separately for each cross, at the same locations. In both populations the analysis of variance indicated significant differences among the groups of the material tested for seed cotton yield, mean boll weight, micronaire reading, staple length, and uniformity ratio. No significant differences were found with respect to plant height, lint percentage, and fiber strength in population I and with respect to lint percentage and fiber strength in population II. In population I, on the basis of mean seed cottonyield and number of superior lines derived by each method as compared to the check varieties and the unselected SSD population, HPS-lines were superior to CPS-lines for seedcotton yield, fiber length and boll weight. HPS-lines, however, did not differ significantly in seedcotton yield from the best check cultivar Eva. Finally, the material derived by CPS was earlier in maturity than the material derived by HPS and SSD. Also in population II, on the basis of mean seedcotton yield and number of superior lines derived by each method as compared to the unselected SSD population, HPS-lines were superior to CPS-lines. No significant differences, however, were identified between the material of the two methods for lint quality traits. It was concluded that in both populations HPS was more effective than CPS in identifying lines with high yielding ability and good lint quality. This superiority of HPS is attributed, at least partially, to its effectiveness in early generation selection. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic variability of heat tolerance, and its effect on yield and fibre quality traits in upland cotton (Gossypium hirsutum L.)

Global temperature is rising because of increasing concentrations of CO₂ and other greenhouse gases (e.g. methane, nitrous oxide, etc.) in the atmosphere because of the excessive use of fossil fuels. High temperature causes heat stress which reduces crop productivity. The development of heat-tolerant varieties is feasible and will help mitigate the effects of climate change. Fifty-one cotton accessions were screened in heat-stressed and non-stressed conditions in the glasshouse and field. Relative cell injury percentage (RCI %), a measure of cell membrane thermostability (CMT), was used to assess heat tolerance. Heat-tolerant accessions had more stable yield and yielded more seed cotton with better quality fibre than the heat-intolerant accessions across four environments. The responses of the 51 accessions to all four environments for the measured traits were strongly associated. RCI % of the accessions and hybrids was strongly and negatively associated with yield and fibre traits. CMT was concluded to be a useful technique for identification of heat-tolerant cotton.     

Drought effects on cotton (Gossypium hirsutum L.) fibre quality and fibre sucrose metabolism during the flowering and boll-formation period

The cotton (Gossypium hirsutum L.) crop is an indeterminate species that is most sensitive to drought stress during the flowering and boll-formation stage of development. To evaluate the effect of water deficit on fibre quality and carbon metabolism at different fruiting branches (FB), multiple controlled experiments were conducted. The cotton cultivar Siza 3 was used under three soil relative water content (SRWC): control (CK, SRWC (75 ± 5) %), moderate drought stress (MDS, SRWC (60 ± 5) %) and severe drought stress (SDS, SRWC (45 ± 5) %) treatment, imposed at the beginning of the flowering of FB_6–7. Fibre quality was significantly affected by drought level and fruiting branch location on the plant. Compared to the CK, under MDS and SDS, sucrose content and sucrose synthase (SuSy) activity decreased prior to 24 days post-anthesis (DPA; the fibre elongation phase), which caused low fibre turgor pressure. This decreased the rate of fibre elongation and final fibre length. Moreover, from 24 to 38 DPA (during fibre thickening), low fibre sucrose content led to insufficient UDP-glucose (UDPG; uridine diphosphate glucose) for cellulose synthesis. Furthermore, more of the existing UDPG was allocated to the synthesis of callose instead of cellulose, which resulted in lower cellulose accumulation and decreased fibre strength. The magnitude of the drought stress effect on fibre qualities, as well as the formation process, was strongly influenced by fruiting branch position, where differences were most pronounced for fruiting branches further away from the base of the plant.     

陆地棉种质资源抗旱性状的关联分析

干旱是导致全世界棉花严重减产、纤维品质下降的重要因素,因此获得高产、优质、耐旱的棉花新品种一直是棉花的育种目标。本研究选取217份陆地棉栽培种组成的自然群体为研究对象,采用全生育期处理组灌水量为对照组50%的干旱胁迫处理,并在处理后期对217份材料的株高、衣分、单铃重等18个性状进行2年2点的表型鉴定,干旱胁迫后,群体间响应差异明显,多个表型性状在对照和处理间表现显著差异。通过BLUP分析表型数据并计算各性状的抗旱系数;全基因组范围选取的214对多态性SSR分子标记扫描群体,共检测到393个多态性位点,基因多样性系数平均值为0.402,范围为0.072～0.631, PIC值平均为0.329,范围为0.070～0.560;群体结构分析表明,该群体可分为2个亚群。用上述SSR标记分别对18个性状的抗旱系数进行关联分析,共关联到76个极显著位点(P<0.01),表型变异解释率为2.930%～7.218%,其中共有14个标记位点能同时被2种或以上性状检测到。研究结果可为后期棉花杂交育种亲本选择及抗旱分子标记辅助育种提供理论基础及参考依据。     

Breeding for high yield and fibre quality in coloured cotton

In the present study, three types of coloured fibre cottons, i.e. white, brown and green, were compared for their fibre quality and yield. The comparison of fibre quality suggested that coloured fibre cotton was inferior as compared with white fibre cotton. To understand the effect of cellulose, mineral elements [nitrogen (N), phosphorus (P) and potassium (K)] and pH of fibre cells on the quality of fibre, these components were studied at different fibre cell developed stages in all three fibre cotton types. The cellulose content is closely associated with the quality of fibre. The higher fibre quality of white fibre cotton might be the result of the high cellulose content in it compared with coloured fibre cotton. A rapid and slow decrease in pH in white and coloured cottons, respectively, might have some effects on fibre elongation. Among the mineral contents, potassium is positively correlated with the fibre quality traits. The pigment development patterns in brown and green fibre cottons are not similar. In green fibre cotton it takes more time to deepen in colour as compared with brown fibre cotton. Possible strategies for the improvement in quality of coloured fibre cotton are discussed. The results of heterosis studies in coloured fibre cotton suggest that heterosis could improve yield and quality of coloured fibre cotton. In the present study, the hybrids between ZJU12A x ZJU05R and ZJU18A x ZJU01R, having an acceptable lint colour types plus better fibre quality and high yield performance, may be exploited further for their heterotic advantages.     

Association analysis of fibre traits in Gossypium arboreum accessions

Advances in the use of diploid Asiatic species in cotton breeding require an understanding of the relatedness and ancestry of diploid cotton accessions, and identification of simple sequence repeat (SSR) markers associated with agronomically important phenotypic traits, for example, fibre quality. Fifty‐six Gossypium arboreum germplasm accessions introduced from nine regions of Africa, Asia and Europe were evaluated for eight fibre characters (lint percentage, lint colour, elongation, micronaire, strength, 50% span length, 2.5% span length and maturity%) and genotyped with 98 SSR markers. When viewed across all accessions most of the SSR markers were polymorphic. Population structure analysis identified six main clusters for the accessions which corresponded to different geographic regions, indicating agreement between genetic and predefined populations. The general linear model method was used to disclose marker–trait associations. Marker–trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with correction for population structure. This paper illustrates the potential of association mapping in diploid cotton, because existing phenotypic data, a modest number of SSR markers, and a pioneering statistical analysis, identified interesting associations.     

Genetic association of within‐boll yield components and boll morphological traits with fibre properties in upland cotton (Gossypium hirsutum L.)

Knowledge of genetic relationships between within‐boll yield components and fibre quality is essential for simultaneous improvement of lint yield and fibre quality in upland cotton (Gossypium hirsutum L.). Nine parents and their F₁ progeny with reciprocals from a 3 × 6 factorial mating design were grown in 2008 and 2009. Seven within‐boll yield components and two boll morphological traits and the three fibre quality parameters were analysed based on a conditional additive/dominance (AD) genetic model. Results showed that boll length contributed to the largest proportion of phenotypic, additive and dominance variances for UHM length; seed index contributed to the largest proportion of phenotypic and additive variances for fibre strength; boll width made the largest contribution to phenotypic and additive variances and the second largest contribution to dominance‐by‐environment interaction variance for micronaire, indicating that they played an important role than the other traits for fibre length, strength and fineness/maturity, respectively. It is worthy of note that those correlations between boll shape and fibre quality apply only to the nine parents and the resultant hybrids in this study and do not imply a cause and effect relationship.     

Genetic effects and heterosis of within-boll yield components in upland cotton (Gossypium hirsutum L.)

Within-boll yield components are the most basic contributors to lint and seed yield of cotton (Gossypium hirsutum L.), which is a major source of natural fiber and edible oil throughout the world. Little information is available on genetic effects and heterosis of these traits in cotton. Three cotton cultivars and six breeding lines differing in within-boll yield components were used for this study. Parents and their F₁ progeny with reciprocals from a 3×6 factorial mating design were grown at Jiangxi Agricultural University experimental farm in 2008 and 2009. Seven within-boll yield components and two boll bur characters were analyzed under an additive-dominance genetic model with genotype and environment interaction. Additive effects were significant for all traits and dominance effects were significant for all traits except seed mass per seed. Genetic variances for lint mass per seed, SM/S and boll bur weight were primarily additive variances ranging from 39.6 to 58.9 %. Lint mass per boll and seed number per boll variances were primarily due to dominance genetic effects ranging from 36.4 to 48.8 %. Dominance and additive effects were equally important for boll weight, seed mass per boll and boll bur percentage. Additive and additive × environment effects were more important than other effects for lint percentage. A802-1 had the best mean performance and additive effects increasing BW, SM/B, S/B and SM/S, but reduced LP and LM/S. A9-1 and Lu40534 had additive effects associated with increasing LP. The two crosses A9-1×Lu40534 and Tezsh×33B were detected with favorable heterozygous dominant effects and heterosis over best parent for BW, LP, LM/B, SM/B and S/B. Favorable genotypic and phenotypic correlations were identified between within-boll lint yield components (LM/B, LM/S) and within-boll seed yield components (SM/B, S/B, SM/S). These results indicate that simultaneous genetic improvement of multiple within-boll yield components can be expected in breeding populations derived from these cotton cultivars and breeding lines.     

Analysis of decision-making coefficients of the lint yield of upland cotton (Gossypium hirsutum L.)

Cold water irrigation and growth in low temperature phytotron are two commonly used methods to evaluate cold tolerance of rice at the seedling stage and the cold sensitive seedlings exhibit different injury symptoms, respectively. However, so far no one has systematically dissected the differences of cold tolerance at seedling stage in rice under the two cold environments. We used a recombinant inbred line (RIL) population derived from a cross of a cold-tolerant japonica cultivar, Lijiangxintuanheigu and a cold sensitive indica cultivar, Sanhuangzhan-2 for this study. The cold sensitive seedlings exhibited leaf yellowing after cold water irrigation and leaf rolling during growth in the low temperature phytotron. Leaf yellowing and leaf rolling in RILs was significantly correlated, but the correlation coefficient was low. A total of four quantitative trait locus (QTLs) on chromosomes 1, 6, 9 and 12 were detected using leaf yellowing and percent seedling survival as indicators of cold tolerance after cold water irrigation, while five QTLs on chromosomes 7, 8, 9, 11 and 12 were detected using leaf rolling and percent seedling survival as indicators of cold tolerance during growth in the low temperature phytotron. The two QTLs, qCTS-9 and qCTS-12 were detected using different evaluation indicators under the two cold environments. Our results suggest that rice cold tolerance mechanisms at the seedling stage differ between the two environments, but the detection of common QTL implies the existence of overlap in the metabolic pathways for cold tolerance. The two common QTLs have potential value in rice breeding.     

QTL analysis for early-maturing traits in cotton using two upland cotton (Gossypium hirsutum L.) crosses

Making use of the markers linked closely to QTL for early-maturing traits for MAS (Marker-assisted selection) is an effective method for the simultaneous improvement of early maturity and other properties in cotton. In this study, two F₂ populations and their F_2:3 families were generated from the two upland cotton (Gossypium hirsutum L.) crosses, Baimian2 × TM-1 and Baimian2 × CIR12. QTL for early-maturing traits were analyzed using F_2:3 families. A total of 54 QTL (31 suggestive and 23 significant) were detected. Fourteen significant QTL had the LOD scores not only > 3 but also exceeding permutation threshold. At least four common QTL, qBP-17 for bud period (BP), qGP-17a/qGP-17b (qGP-17) for growth period (GP), qYPBF-17a/qYPBF-17b (qYPBF-17) for yield percentage before frost (YPBF) and qHFFBN-17 for height of first fruiting branch node (HFFBN), were found in both populations. These common QTL should be reliable and could be used for MAS to facilitate early maturity. The common QTL, qBP-17, had a LOD score not only > 3 but also exceeding permutation threshold, explaining 12.6% of the phenotypic variation. This QTL should be considered preferentially in MAS. Early-maturing traits of cotton are primarily controlled by dominant and over-dominant effects.     

Diallel analysis of yield components,fibre quality and bacterial blight resistance using spaced plants of cotton

Summary Hayman analysis for lint percentage, boll weight, fibre quality and bacterial blight resistance of a ten-parent half-diallel set of crosses was conducted in Upland cotton. The ten parents represented a fixed sample of the best germplasm available to Australian breeders for the characters of commercial importance. Heterosis and inbreeding depression were detected particulady for boll weight and blight resistance. An analysis of genetic components and parameters indicated that since additive effects were substantial and heritability high, early-generation selection of spaced plants and pure-line breeding should be successful. Some genotypes were identified as being potentially good donors for hybridization since they possessed dominant genes for improved character expression. Acala C-1 was identified as the first-choice parent for increased boll size. Coker 315 for increased span length, while Namcala was the best parent for breeding improved fibre strength. McNair 220 possessed the most dominant genes for high lint percentage. Reba P279 and Siokra were the only parents with resistance to the prevelant race of bacterial blight.     

Genetic analysis of agronomic and fibre traits using four interspecific chromosome substitution lines in cotton

Backcrossed chromosome substitution lines (CS‐B) have been developed with a homologous pair of chromosomes or chromosome arms of Gossypium barbadense (3‐79) germplasm substituted for the homologous Gossypium hirsutum(TM‐1) chromosomes or chromosome segments. We report on agronomic and fibre trait performance of four backcrossed chromosome or chromosome arm substitution lines including chromosomes 01, 11sh (chromosome 11 short arm), 12 sh and 26 Lo (chromosome 26 long arm). Data for agronomic and fibre traits were collected from replicated field experiments at two different locations in 2 years, and analysed under an additive dominance genetic model. CS‐B 12sh had higher, while CS‐B 01 and CS‐B 26Lo had lower boll weight than TM‐1. The presence of significant negative additive effects for micronaire with CS‐B 01 and significant positive additive effects for elongation and fibre strength with CS‐B 11sh suggested the substituted chromosome arms of 3‐79 in these CS‐B lines were more likely carrying genes causing these effects. Results revealed that several CS‐B lines had significant homozygous and heterozygous dominance effects for different agronomic and fibre traits suggesting that specific CS‐B lines may be useful for improving agronomic and fibre traits in hybrid cottons. These CS‐B lines also provide novel genetic resources for improving upland cotton germplasm.     

Density responses and spatial distribution of cotton yield and yield components in jujube (Zizyphus jujube)/cotton (Gossypium hirsutum) agroforestry

Trees are the dominant species in agroforestry systems, profoundly affecting the performance of understory crops. Proximity to trees is a key factor in crop performance, but rather little information is available on the spatial distribution of yield and yield components of crop species under the influence of trees in agroforestry systems. Also, little information is available on how crop density may be exploited to optimize the yield in such systems. Here we studied the performance of cotton in jujube/cotton agroforestry. Field experiments were conducted in 2012 and 2013 in Hetian, Xinjiang, China. Cotton was grown at a row distance of 60 cm in three densities, 13.5, 18.0 and 22.5 plants m⁻² in six m wide paths between tree lines in a jujube plantation. Plant density affected both cotton aboveground dry matter and yield significantly. The highest yield was attained at the intermediate density of 18.0 plants m⁻² (20.0 plants m⁻² corresponding in sole cotton), lower than the optimal density in sole cotton (25.0 plants m⁻²). Yield at the lower density was constrained by the low number of bolls per m² as a direct consequence of the low density, whereas at the high plant density yield was constrained by a lower allocation of assimilates to cotton seed and lint, as a consequence of intraspecific and interspecific competitions. There were strong gradients in yield and yield components in relation to the distance from the tree rows. Leaf area and total dry matter of cotton in rows close to the tree lines were reduced, especially in the rows next to the trees. Moreover, biomass allocation to cotton fruits was reduced in these rows. Competitive influences from the trees on cotton performance extended two rows deep in a six-year old jujube stand, and even three rows deep in a seven-year old stand. Shading effects on cotton yield were compensated by increasing plant density as a result of greater boll numbers per unit ground area. Data from this study help guide the design of optimal plant density of cotton in jujube plantations and give insight in the spatial distribution and dynamics of competitive effects in agroforestry systems in general.     

Genome mapping and molecular markers identification for yield,yield component and fibre quality traits in tetraploid cotton

The identification of quantitative trait loci (QTL) across different environments is a prerequisite for marker‐assisted selection (MAS) in crop improvement programmes. CottonSNP63k Illumina infinium array was used for genotyping 178 inter‐specific recombinant inbred lines and the parents, and identified 1,667 homozygous polymorphic markers between the parents. Of these, 1,430 markers were used for the construction of linkage map after removing 237 redundant markers. The genetic map spans a total genetic length of 3,149.8 cM with an average marker interval size of 2.2 cM. The phenotypic data from five environments were analysed separately using inclusive composite interval mapping which identified a total of 56 QTL explaining phenotypic variances (PVE) in the range of 8.18%–28.91%. There were 11 and 24 major QTL found for fibre quality and yield components, respectively. A total of 64 QTL were identified through Multi‐Environment Trials analysis, of which 34 recorded QTL × Environment interactions.