SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height

Abstract

Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of phenotypic variation (R 2), respectively. The qtph1.1 was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40), Solyc01g098390 encoding GA receptor SlGID1a was the putative candidate gene. The SlGID1a gene underlying the qtph1.1 locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the qtph1.1 locus (NIL-qtph1.1) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL-qtph1.1 could not be rescued by exogenous GA 3 treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL-qtph1.1 and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height.

SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway

“…Height is one of the most important agronomic traits for crops, and affects plant architecture, soil utilization rate, nutrition management, and production management [ 1 , 55 ]. In this study, we found that the C2H2 zinc-finger transcription factor SlZF3 regulates tomato plant height via the GA pathway.…”

“…Plant height is one of the most important agronomic traits in crops, which is especially evident in the Green Revolution in cereal crops. It affects crop architecture, land utilization, nutrition, and production management [ 1 ]. Plant height is controlled by many genes, especially those related to plant hormone biosynthesis or signal transduction, including gibberellic acid (GA), auxin, brassinosteroid, and strigolactone [ 2–5 ].…”

Quantitative Trait Loci Mapping for Bacterial Wilt Resistance and Plant Height in Tomatoes

“…Plant height (PH) is an important agronomic trait in crops. Height can impact the architecture of plants, nutrient and water management, and mechanical harvest ability, which ultimately affects the quality and yield [ 45 ]. In fresh-market tomatoes, a compact growth habit is desirable because it enables mechanical harvesting [ 45 , 46 , 47 ].…”

“…PH is a quantitative trait. Several QTLs have been identified related to PH in tomatoes [ 45 ]. A study detected nine QTLs ( ht1 , ht3 , ht5a , ht5b , ht6 , ht7 , ht9 , ht10 , and ht11 ) linked to PH using a segregating population developed from a cross between interspecies tomatoes (vendor Tm-a2 and LA716) [ 48 ].…”

“…QTLs have reportedly controlled PH on chromosomes 3, 4, 9, 11, and 12 in 20 introgression lines derived from Solanum chmielewskii introgression into S. lycopersicum [ 51 ]. More recently, three QTLs h4t2a , h4t3a , and h4t7a were reportedly linked to PH in an introgression line population derived from Solanum pennellii (LA0716) introgression into an inbred line (1052) [ 45 , 52 ], and seven QTLs related to PH were detected on chromosomes 1, 3, 5, 9, 10, 11, and 12 in an F 2 population. However, the PH QTLs have not been mapped using SNP-based molecular maps, which can facilitate robust marker development for selection.…”