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. 2018 Oct 29;19(1):776.
doi: 10.1186/s12864-018-5129-4.

Integration of conventional and advanced molecular tools to track footprints of heterosis in cotton

Zareen Sarfraz  1 , Muhammad Shahid Iqbal  1   2 , Zhaoe Pan  1 , Yinhua Jia  1 , Shoupu He  1 , Qinglian Wang  3 , Hongde Qin  4 , Jinhai Liu  5 , Hui Liu  6 , Jun Yang  7 , Zhiying Ma  8 , Dongyong Xu  9 , Jinlong Yang  5 , Jinbiao Zhang  10 , Wenfang Gong  1 , Xiaoli Geng  1 , Zhikun Li  8 , Zhongmin Cai  5 , Xuelin Zhang  11 , Xin Zhang  3 , Aifen Huang  12 , Xianda Yi  4 , Guanyin Zhou  5 , Lin Li  10 , Haiyong Zhu  1 , Yujie Qu  1 , Baoyin Pang  1 , Liru Wang  1 , Muhammad Sajid Iqbal  1 , Muhammad Jamshed  1 , Junling Sun  13 , Xiongming Du  14
Affiliations

Integration of conventional and advanced molecular tools to track footprints of heterosis in cotton

Zareen Sarfraz et al. BMC Genomics. .

Abstract

Background: Heterosis, a multigenic complex trait extrapolated as sum total of many phenotypic features, is widely utilized phenomenon in agricultural crops for about a century. It is mainly focused on establishing vigorous cultivars with the fact that its deployment in crops necessitates the perspective of genomic impressions on prior selection for metric traits. In spite of extensive investigations, the actual mysterious genetic basis of heterosis is yet to unravel. Contemporary crop breeding is aimed at enhanced crop production overcoming former achievements. Leading cotton improvement programs remained handicapped to attain significant accomplishments.

Results: In mentioned context, a comprehensive project was designed involving a large collection of cotton accessions including 284 lines, 5 testers along with their respective F1 hybrids derived from Line × Tester mating design were evaluated under 10 diverse environments. Heterosis, GCA and SCA were estimated from morphological and fiber quality traits by L × T analysis. For the exploration of elite marker alleles related to heterosis and to provide the material carrying such multiple alleles the mentioned three dependent variables along with trait phenotype values were executed for association study aided by microsatellites in mixed linear model based on population structure and linkage disequilibrium analysis. Highly significant 46 microsatellites were discovered in association with the fiber and yield related traits under study. It was observed that two-thirds of the highly significant associated microsatellites related to fiber quality were distributed on D sub-genome, including some with pleiotropic effect. Newly discovered 32 hQTLs related to fiber quality traits are one of prominent findings from current study. A set of 96 exclusively favorable alleles were discovered and C tester (A971Bt) posited a major contributor of these alleles primarily associated with fiber quality.

Conclusions: Hence, to uncover hidden facts lying within heterosis phenomenon, discovery of additional hQTLs is required to improve fibre quality. To grab prominent improvement in influenced fiber quality and yield traits, we suggest the A971 Bt cotton cultivar as fundamental element in advance breeding programs as a parent of choice.

Keywords: Cotton; Favorable alleles; Fiber quality; GCA; Heterosis; L × T; Microsatellite markers; SCA; hQTL.

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Conflict of interest statement

Ethics approval and consent to participate

Ethics approval does not apply to this study as it has not directly involved humans or animals. The seed material used in this study was taken from Gene Bank of Institute of Cotton Research (ICR), Chinese Academy of Agricultural Sciences (CAAS). The field experiments were conducted in accordance with the institutional and national guidelines set for the research station/institutes involved in the current study. There was no need to get specific/additional permission to conduct the field research or genotyping analyses. The field studies did not involve endangered or protected species.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Correlogram for fiber quality traits in F1s and Parents of upland cotton. The density distribution of each variable for F1s and Parents is shown at diagonal with distinct colors (blue: F1s, orange: Parents). On the lower side, the bivariate scatter plots are displayed while on the upper side, the values along with significance (*) of correlation coefficients for variables of F1 s and Parents are presented. Boxplots illustrating the variability among individuals of parents and offsprings. The central box represents the middle half data lengthening from upper to lower quartile while the horizontal line is located at median. The ends point of vertical projections specify maximum and minimum data points, unless the presence of outliers. Solid dots at upper and lower sides represents outliers. The bottom most rows depicted frequency distribution of each variable for F1s and Parents
Fig. 2
Fig. 2
Scatter diagram of F1s and Parents in upland cottons based on phenological data projected in the (Dim1-Dim2) plane. Different colours depicting the distinct groups of lines, testers, F1s and checks. Abbreviations: Dim1., PC-1; Dim2., PC-2; A., 7886 tester; B., Zhong 1421 tester; C., A971 Bt tester; D., 4133 Bt tester; E., SGK 9708 tester
Fig. 3
Fig. 3
a, b, c, d, e, f The summary plots of Q-matrix estimates based on Bayesian posterior probability and Line charts of K with respect to SK for F1s from A, B, C, D and E male parents and 284 Female parents respectively. g, h, i, j, k, l SK values exhibited a maximum likelihood at K = 3 in Female parents (suggesting the total panel division into three subpopulations) while K = 2 in all the F1 hybrids
Fig. 4
Fig. 4
a, b, c, d, e, f Linkage disequilibrium distribution patterns between all possible loci pairs of female parents and F1s, Set-A, set-B, set-C, set-D, set-E respectively across various chromosomes. Each pixel on upper side of diagonal indicates size of D′ related to corresponding marker pair as revealed with the color code at top right; whereas lower side of diagonal specifies P value of respective marker pair LD as revealed with the color code at the bottom right: white p > 0.05, blue 0.05 > p > 0.01, green 0.01 > p > 0.001 and red p < 0.001. g, h, i, j, k, l Scatterplots of the significant LD (r2) against physical distance (Mb) of female parents and F1 set-A, set-B, set-C, set-D, set-E respectively. The trend line (inner fitted) is a logarithmic regression curve based on r2 against physical distance
Fig. 5
Fig. 5
Summary of contributions delivered by dependent variables under study: trait phenotype, heterosis, specific combining ability (SCA) and General combining ability (GCA) for discovering significant (−log10 > 3) associations in L × T mating design. Size of each block is depiction of amount of significant associations in respective category of combinations. Abbreviations: A., Genotype & phenotype data of F1s from 7886 (A) tester; B., Genotype & phenotype data of F1s from Zhong 1421 (B) tester; C., Genotype & phenotype data of F1s from A971 Bt (C) tester; D., Genotype & phenotype data of F1s from 4133 Bt (D) tester; E., Genotype & phenotype data of F1s from SGK 9708 (E) tester; PA., Genotype data of maternal lines-phenotype data of F1s from 7886 (A) tester; PB., Genotype data of maternal lines-phenotype data of F1s from Zhong 1421 (B) tester; PC., Genotype data of maternal lines-phenotype data of F1s from A971 Bt (C) tester; PD., Genotype data of maternal lines-phenotype data of F1s from 4133 Bt (D) tester; PE., Genotype data of maternal lines-phenotype data of F1s from SGK 9708 (E) tester; PS., Genotype & phenotype data of Parents (Females)
Fig. 6
Fig. 6
Significant associations (-log10>3) of (a) Fiber Uniformity Index (FUI), (b) Lint Percentage (LP), (c) Fiber Strength (FS), (d) Fiber Length (FL), (e) Boll Weight (BW), (f) Fiber Fineness (MIC), (g) Fiber Elongation (FE), (h) Plant Height (PH) and (i) Fiber Uniformity (FU) with microsatellites displaying their respective phenotypic effects. Color shading indicates an individual dependent variable that is Phenotype, SCA, GCA and Heterosis types. Abbreviations: A.,7886; B., Zhong 1421; C., A971 Bt; D., 4133 Bt; E., SGK 9708
Fig. 7
Fig. 7
Summary of significantly (p < 0.001) associated microsatellites with phenotypic traits based on their distribution on A and D sub-genomes. Eight phenotypic traits found their significant associations with 15 microsatellites distributed on A sub-genome and 8 phenotypic traits got significant associations with 31 microsatellites from D sub-genome
Fig. 8
Fig. 8
Power for detection of hQTLs in significant (−log10 > 3) associations ranked according to amount of associations detected. Viscosity of each originating link is indicating the power of hQTL detection in terms of association numbers. Abbreviations: HB., Heterobeltosis; HI., Heterosis Index; MP., Mid-Parent Heterosis; K3., Heterosis over Check K3; K4., Heterosis over Check K4; AM., Genotype & phenotype data of F1s from 7886 (A) tester; BM., Genotype & phenotype data of F1s from Zhong 1421 (B) tester; CM., Genotype & phenotype data of F1s from A971 Bt (C) tester; DM., Genotype & phenotype data of F1s from 4133 Bt (D) tester; EM., Genotype & phenotype data of F1s from SGK 9708 (E) tester; PA., Genotype data of maternal lines & phenotype data of F1s from 7886 (A) tester; PB., Genotype data of maternal lines & phenotype data of F1s from Zhong 1421 (B) tester; PC., Genotype data of maternal lines & phenotype data of F1s from A971 Bt (C) tester; PD., Genotype data of maternal lines & phenotype data of F1s from 4133 Bt (D) tester; PE., Genotype data of maternal lines & phenotype data of F1s from SGK 9708 (E) tester; PS., Genotype & phenotype data of maternal lines
Fig. 9
Fig. 9
Favorable alleles of significant (-log10>3) QTLs for (a) Plant Height (PH), (b) Fiber Uniformity Index (FUI), (c) Lint Percentage (LP), (d) Fiber Uniformity (FU), (e) Fiber Strength (FS), (f) Fiber Length (FL), (g) Fiber Elongation (FE), (h) Fiber Fineness (MIC), (i) Boll Weight (BW), (j) Boll Number (BN) with their respective phenotypic effects (ai). Representative combinations of phenotype and genotype data used in TASSEL association analysis with abbreviation: A., Genotype & phenotype data of F1s from 7886 tester; B., Genotype & phenotype data of F1s from Zhong 1421 tester; C., Genotype & phenotype data of F1s from A971 Bt tester; D., Genotype & phenotype data of F1s from 4133 Bt tester; E., Genotype & phenotype data of F1s from SGK 9708 tester; PA., Genotype data of maternal lines-phenotype data of F1s from 7886 tester; PB., Genotype data of maternal lines-phenotype data of F1s from Zhong 1421 (B) tester; PC., Genotype data of maternal lines-phenotype data of F1s from A971 Bt tester, PD., Genotype data of maternal lines-phenotype data of F1s from 4133 Bt (D) tester; PE., Genotype data of maternal lines-phenotype data of F1s from SGK 9708 tester
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