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Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Malus × domestica Borkh.)

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Abstract

Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple.

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Acknowledgements

The authors are grateful to the Indian Council of Agricultural Research (ICAR), New Delhi, India for proving funds through a central assistance scheme.

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Authors and Affiliations

  1. Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP, 173 230, India

    Poonam, Rajnish Sharma & Parul Sharma

  2. Department of Fruit Science, Dr YS Parmar University of Horticulture & Forestry, Solan, HP, 173 230, India

    Naveen C. Sharma

  3. ICAR-Indian Institute of Pulses Research, Kanpur, UP, 208 024, India

    Kuldeep Kumar

  4. Department of Botany, University of Delhi, North Campus, New Delhi, India

    Krishna Nand Singh

  5. ICAR-Central Potato Research Institute, Shimla, HP, 171 004, India

    Vinay Bhardwaj

  6. ICAR-NBPGR Regional Station, Phagli, Shimla, HP, 171 004, India

    Narender Negi

  7. RHR&TS, Dr YS Parmar University of Horticulture & Forestry, Mashobra, Shimla, HP, 171 007, India

    Neena Chauhan

  8. School of Bioengineering & Food Technology, Shoolini University, Solan, HP, 173 229, India

    Poonam

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Contributions

Germplasm collection, investigation, data compilation, writing—original draft preparation: P; Conceptualization, methodology, overall supervision, manuscript editing and finalization: RS; SSR analysis, manuscript reviewing, editing and finalization: PS; Physico-chemical characterization: NCS; Association mapping data analysis and manuscript finalization: KK, KNS and VB; Germplasm maintenance: NG, NC.

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Correspondence to Rajnish Sharma.

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12298_2023_1382_MOESM1_ESM.tif

Fig S1 Regression plot showing the relationships between fruit length and other measured variables significant at P<0.05 and marginally significant at P<0.10. The units are scaled and centered (TIF 389 KB)

12298_2023_1382_MOESM2_ESM.tif

Fig S2 Regression plot showing the relationships between fruit diameter and other measured variables significant at P<0.05 and marginally significant at P<0.10.The units are scaled and centered (TIF 364 KB)

12298_2023_1382_MOESM3_ESM.tif

Fig S3 Regression plot showing the relationships between fruit weight, fruit shape index, firmness and other measured variables significant at P < 0.05 and marginally significant at P < 0.10. The units are scaled and centered (TIF 521 KB)

12298_2023_1382_MOESM4_ESM.tif

Fig S4 Regression plot showing the relationships between, TSS, total sugar, reducing sugar and acidity and other measured variables significant at P < 0.05 and marginally significant at P < 0.10.The units are scaled and centered (TIF 520 KB)

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Poonam, Sharma, R., Sharma, P. et al. Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple (Malus × domestica Borkh.). Physiol Mol Biol Plants 29, 1693–1716 (2023). https://doi.org/10.1007/s12298-023-01382-w

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