Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.)

Area of Science:

• Plant genetics
• Molecular biology
• Agricultural science

Background:

• Leaf margin phenotypes in pineapple (Ananas comosus var. comosus) are important traits for breeding.
• Understanding the genetic basis of these phenotypes is crucial for developing improved cultivars.

Purpose of the Study:

• To identify genome-wide DNA polymorphisms.
• To develop DNA markers for leaf margin phenotypes in pineapple.
• To map these DNA markers relative to known genes controlling leaf shape.

Main Methods:

• Restriction-site-associated DNA sequencing (RAD-seq) analysis of F1 progeny from a cross between 'piping-leaf' and 'spiny-tip-leaf' pineapple cultivars.
• Conversion of identified RAD-seq tags into Cleaved Amplified Polymorphic Sequence (CAPS) and Simple Sequence Repeat (SSR) markers.
• Genotyping of F1 progeny and linkage analysis to map the developed markers.

Main Results:

• Identified piping-leaf (PLSTs) and spiny-tip-leaf (STSLTs) gene-specific RAD-seq tags.
• Developed five PLSTs and two STSLTs into functional CAPS or SSR markers.
• Mapped five PLST markers near the P locus (closest at 1.5 cM) and two STLST markers near the S locus (2.2 cM).
• Demonstrated that the developed markers accurately distinguish between leaf margin types.

Conclusions:

• Developed SSR and CAPS markers are effective for identifying DNA polymorphisms associated with leaf margin phenotypes in pineapple.
• These markers are valuable tools for marker-assisted selection in pineapple breeding programs aimed at controlling leaf morphology.