A high-density linkage map construction in guava (Psidium guajava L.) using genotyping by sequencing and identification of QTLs for leaf, peel, and pulp color in an intervarietal mapping population

Malarvizhi Mathiazhagan; Dayanandhi Elangovan; Vasugi Chinnaiyan; Kodthalu Seetharamaiah Shivashankara; Darisi Venkata Sudhakar Rao; Kundapura Venkataramana Ravishankar

doi:10.3389/fpls.2024.1335715

A high-density linkage map construction in guava (Psidium guajava L.) using genotyping by sequencing and identification of QTLs for leaf, peel, and pulp color in an intervarietal mapping population

Front Plant Sci. 2024 Feb 27:15:1335715. doi: 10.3389/fpls.2024.1335715. eCollection 2024.

Authors

Malarvizhi Mathiazhagan^{1

2}, Dayanandhi Elangovan¹, Vasugi Chinnaiyan³, Kodthalu Seetharamaiah Shivashankara¹, Darisi Venkata Sudhakar Rao⁴, Kundapura Venkataramana Ravishankar¹

Affiliations

¹ Division of Basic Sciences, ICAR-Indian Institute of Horticultural Research, Bengaluru, India.
² Centre for Post-graduate Studies, Jain (Deemed-to-be) University, Bengaluru, India.
³ Division of Fruit Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, India.
⁴ Division of Post Harvest Technology and Agricultural Engineering, ICAR-Indian Institute of Horticultural Research, Bengaluru, India.

Abstract

Psidium guajava L. is an important fruit crop in the tropical and subtropical regions of the world. The advanced breeding methods are not employed for important commercial traits like peel and pulp color, seed hardiness, fruit size, etc., due to the scarcity of genome-wide molecular markers and high-density linkage maps. In this study, we employed single-nucleotide polymorphism (SNP) markers and identified quantitative trait loci (QTL) regions that are associated with color traits of leaf, peel, and pulp in the guava intervarietal mapping population. The mapping population was developed from the contrasting genotypes of fruit and leaf color. Variations in color among the segregating hybrids were recorded both visually and using a Color reader. A high-density linkage map of guava was constructed using the SNP markers from genotyping by sequencing (GBS) of 150 hybrid individuals of the cross 'Arka Poorna' (green) x 'Purple Local' (purple). The integrated linkage map consisted of 1426 SNPs mapped on 11 linkage groups (LG), spanning a total distance of around 730 cM with an average of 129.6 markers per LG. Through QTL analysis for color traits, a minor QTL region was identified for visually scored leaf color and peel color on LG1, whereas a major QTL was detected for pulp color in LG4. The Hunter color values (L* and, a*) also had major QTLs with overlapping marker intervals for leaf and peel colors, establishing the association of SNP markers to the trait. The QTLs harbored genes and transcription factors involved in lycopene and anthocyanin pigment biosynthesis. This is the first report of a high-density linkage map based on SNP markers in guava and QTL mapping for color characters in leaf, fruit peel and pulp. The genotyping information generated in this study can aid in genetic engineering and marker-assisted breeding in guava.

Keywords: SNP markers; genotyping by sequencing; guava; leaf color; linkage map; peel color; pulp color; quantitative trait loci.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The financial support received from Rashtriya Krishi Vikas Yojana (RKVY) project, “Centre for excellence in genomic assisted selection for developing processing guava” (Grant ID-KA/RKVY-HORT2022/1299).