AUTHOR=Nimmakayala Padma , Tomason Yan R. , Abburi Venkata L. , Alvarado Alejandra , Saminathan Thangasamy , Vajja Venkata G. , Salazar Germania , Panicker Girish K. , Levi Amnon , Wechter William P. , McCreight James D. , Korol Abraham B. , Ronin Yefim , Garcia-Mas Jordi , Reddy Umesh K. 

TITLE=Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.01437

DOI=10.3389/fpls.2016.01437

ISSN=1664-462X

ABSTRACT=<p>Melon (<italic>Cucumis melo</italic> L.) is a phenotypically diverse eudicot diploid (2<italic>n</italic> = 2<italic>x</italic> = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (<italic>Fst</italic>) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The <italic>F</italic><sub><italic>ST</italic></sub> between accessions of <italic>cantalupensis</italic> and <italic>inodorus</italic> was 0.23. The <italic>F</italic><sub><italic>ST</italic></sub> between <italic>cantalupensis</italic> and various <italic>agrestis</italic> accessions was in a range of 0.19–0.53 and between <italic>inodorus</italic> and <italic>agrestis</italic> accessions was in a range of 0.21–0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.</p>