| Tomato(Solanum Lycopersicum L.) is one of the most important vegetables around the world, and it is also a model species to study fruit development. Tomato fruit weight and fruit shape are important commodity quality traits, and thus become target traits in tomato breeding. Tomato fruit weight and fruit shape are influenced to a certain extent by fruit locule number. Fruit locule number is one of the domestication syndrome traits in tomato, because the fruit locule number of cherry tomato and cultivated tomato varies from two to ten or more, while their wild ancestors usually bear fruit containing two locules. Therefore, discovery of the genetic basis of tomato fruit locule number will not only help to elucidate the molecular mechanism of tomato domestication and fruit development, but also provide the theoretical basis for tomato molecular breeding. Molecular markers play important roles in tomato genetic analysis and breeding. InDel(insertion/deleion) is a kind of conventional marker. In the present study, we developed a collection of InDel markers that was validated with several frequently-used tomato lines via agarose gel electrophoresis. We also fie-mapped locule number 2.2(lcn2.2), a major quantitative trait locus(QTL) controlling fruit locule number, in tomato line T909. The main results obtained in the present study are summarized below:1. 1651 InDel markers were developed in the present study. InDels were identified by comparing the sequence of Heinz 1706, LA1589, LA0716, and the other tomato lines that were re-sequenced. The primers were designed by software Primer3. PCR was carried out on the genomic DNA of 24 frequently-used tomato lines. And then the PCR product was spread via 3% agarose gel electrophoresis. Totally, 1651 InDels showed polymorphism among the 24 tomato lines. These InDel markers were spread out on 12 chromosomes. There were 85, 233, 150, 136, 78, 213, 120, 132, 133, 125, 104 and 142 markers on from chromosome 1 to chromosome 12. Of these markers, 1317 markers, accounting for 79.8%, showed polymorphism among 8 wild tomato lines; 912 markers, accounting for 55.2%, showed polymorphism among 14 cultivated tomato lines; 1638 markers, accounting for 99.2%, showed polymorphism between wild tomato lines and cultivated tomato lines.2. locule number 2.2(lcn2.2), a major QTL controlling fruit locule number, was identified in tomato line T909. T909 is a cultivated tomato line that contains a major QTL locule number(lc) controlling fruit locule number, but the fruit locule number of T909 is much higher than that of many tomato lines which also contain lc locus. Therefore, it is speculated that T909 contains another major QTL controlling fruit locule number. An F2 population containing 220 plants was developed from the cross between T909 and Heinz 1706. DNA bulks from 20 “highest locule number†and 20 “lowest locule number†plants in this F2 poplation was made and re-sequenced. QTL-seq analysis showed that only chromosome 2 contains the QTLs for fruit locule number. At the same time, a BC1S1 population containing 402 plants was developed from the cross between T909 and LA1589. Traditional QTL analysis showed that there were two major QTLs on chromosome 2 in T909. They were overlapped with lc and lcn2.2, respectively. lcn2.2 locus which was identified in T909 was located in the region of 58.7–52.9 Mb on chromosome 2. It could explain up to 23.8% phenotypic variant(R2=0.238).3. lcn2.2 was fine-mapped to a 345 kb region containing 41 putative genes on chromosome 2. Several recombinants, whose cross over site was in the region of 58.7–52.9 Mb on chromosome 2, were identified in BC1S1 and BC1S2 poplations, and then were progeny tested. The result suggested that lcn2.2 was located in a 345 kb region between InDel marker C02M51897 and C02M52241. The physical position of this region was SL2.50ch02: 51,897,315-52,241,826. Forty-one putative genes were found in this region by searching the tomato genome annotation database(ITAG release2.40) in SGN(https://solgenomics.net/). |
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