| Popcorn is a special kind of corn type used to make popcorn flake for a series pastime foodstuff, it has unique values in the snack-food industry. Popping characteristics and grain yield are important traits in maize breeding. They are all quantitative trait controlled by multiple genes. Domestic and foreign breeders have conducted lots of researches in germplasm improvement and traditional quantitative genetics. But few researches have been done in the molecular quantitative genetics for most characters in popcorn. In this research, two hundred and fifty-eight RILs were developed from a cross between a dent corn indred, Dan232, and an elite popcorn indred, N04. A high-density genetic map was constructed using SSR markers. Three popping characteristics, 8 ear-kernel traits, 9 plant traits and 4 kernel nutritive characters were evaluated. High-density genetic maps were constructed using SSR markers. QTL analyses were conducted by composite interval mapping (CIM) method and the LOD threshold values were determined by 1000 times permutation test. The interactions of detected QTL were identified using multiple interval mapping (MIM) method according to the result obtained using CIM method. The joint QTL analysis for two or three different traits were done using composite interval mapping (CIM) of multiple traits analysis, including popping characteristics, ear-kernel characters, kernel nutritive characters, and plant characters. This research was to analyze their molecular genetic mechanism and genetic correlations among different characters. Also, stable QTL across different environments and generations could be selected by comparing with its F2:3 and BC2F2 population derived form the same parents. These results provide more reliable theoretical basis and materials for marker-assisted selection, fine mapping, map-based cloning, and other related researches in future.The main results in this study were as follows:1. Totally, 723 SSR primers were selected to screen polymorphism between two parents, N04 and Dan232, 212 markers (29.32%) were in co-dominant segregation. Two hundred and seven pairs SSR markers were selected to construct a genetic linkage map using Mapmaker 3.0 with a total genetic length of 2 408.8 cM and the average interval of 11.64 cM.2. Transgressive segregation were observed for three popping characters, eight ear-kernel characters, nine plant characters and four kernel nutritive characters in the RIL population except for popping fold (PF) and leaves above ear (LNE). Normal distribution was observed for all traits. The heritability of 3 popping characters, 8 ear-kernel characters, 9 plant characters and 4 kernel nutritive characters were all high, ranging from 0.90 to 0.92, 0.83 to 0.94, 0.67 to 0.93 and 0.80 to 0.96, respectively.3. Twenty-seven QTL were detected for 3 popping characters under three environments and in combined analysis. Phenotypic variation explained by a single QTL varied from 4.43% to 20.95%. Of these, 3 QTL (qPF-1-1,qPV-7-1 and qPR-1-1) were common under three different environments and in combined analysis, and 7 QTL explained up to 10% phenotypic variation. Digenic interactions were detected for 12 pairs of QTL or marker intervals. Eight QTL (qPF-1-1, qPF-2-1, qPF-6-2, qPV-1-1, qPV-6-1, qPR-1-1, qPR-6-1, and qPR-6-2) were also detected in the F2:3 population, two QTL (qPF-2-1 and qPV-6-1) were also detected in the BC2F2 population, which were stable between generations.4. Eighty-seven QTL were detected for 8 ear-kernel traits under three environments and in combined analysis, phenotypic variation explained by a single QTL varied from 3.93% to 24.59%. Of these, thirteen QTL (qGW-10-1, qGWP-4-1, qGWP-4-2, qGWP-10-1, q100GW-1-1, q100GW-5-1, q100GW-7-1, qEL-1-1, qEL-1-2, qED-1-1, qERN-4-1, qERN-9-1, and qKR-4-1) were common under three different environments and in combined analysis, and 39 QTL explained up to 10% phenotypic variation. Digenic interactions were detected for 35 pairs of QTL or marker intervals. Six QTL (q100GW-5-1, q100GW-7-1, qEL-3-1, qED-10-2, qERN-4-1, and qERN-10-1) were also detected in the F2:3 population, three QTL (q100GW-5-1, qEL-3-1, and qED-10-1) were also detected in the BC2F2 population. q100GW-5-1 was detected under 3 environments and in all populations, and qEL-3-1 was detected in 3 populations, which showed stability across environments and generations.5. Fifty-two QTL were detected for 4 kernel nutritive characters under three environments and in combined analysis, phenotypic variation explained by a single QTL varied from 4.10% to 16.80%. Of these, eight QTL (qCP-3-1, qCP-4-1, qCT-3-1, qCT-4-1, qCT-5-2, qCT-9-1, qCF-1-1, and qLS-3-1) were common under three or two different environments and in combined analysis, and 6 QTL explained up to 10% phenotypic variation. Digenic interactions were detected for 18 pairs of QTLs or marker intervals. Four QTL (qCP-4-1, qCP-6-1, qCT-3-1, and qCT-4-1) were also detected in the F2:3 population, three QTL (qCP-6-1,qCT-3-1, and qCF-7-2) were also detected in the BC2F2 population. qCT-3-1 was detected under 3 environments and in all populations, and qCP-6-1 was detected in 3 populations, which showed stability across environments and generations.6. One hundred and eighty QTL were detected for 9 plant traits under three environments and in combined analysis, phenotypic variation explained by a single QTL varied from 3.86% to 28.40%. Of these, twenty-seven QTL (qSD-5-2, qPH-1-2, qPH-4-1, qPH-5-1, qPH-7-1, qPH-8-3, qEH-1-1, qEH-3-2, qEH-5-1, qEH-10-1, qTH-5-2, qTH-7-1, qTH-8-1, qTHPH-1-1, qTHPH-10-1, qLNE-5-3, qLNE-6-1, qLA-2-1, qLA-2-2, qLA-4-1, qLA-7-1, qLA-7-3, qLA-8-2, qTL-7-1, qTL-8-2, qTB-4-1, and qTB-8-1) were common detected under three or two different environments and in combined analysis, sixty QTL explained up to 10%; Digenic interactions were detected for 54 pairs of QTL or marker intervals. Fifteen QTL (qPH-7-1, qPH-7-2, qPH-8-3, qPH-9-1, qEH-3-2, qTH-8-1, qTHPH-3-1, qTHPH-3-2, qLNE-3-4, qLNE-5-2, qLA-4-1, qLA-7-2, qLA-8-2, qTL-6-1, and qTB-10-1) were also detected in F2:3 population, ten QTL(qPH-1-2, qPH-8-3, qTH-1-1, qTH-7-1, qTH-8-1, qTHPH-3-1, qTHPH-10-1, qTL-4-3, qTL-8-2 and qTB-10-1) were also detected in BC2F2 population. qPH-8-3, qTH-8-1, qTHPH-3-1 and qTB-10-1 were detected under 3 environments and in all populations, and qPH-8-3, qTH-8-1, and qTHPH-3-1 were detected in 3 populations, which showed stability across environments and generations.7. Relationships between 4 kind of traits were consistent under 3 environments. Significant positive correlations were observed among 3 popping characters. 100GW was positively correlated with ERN and RKN, PH was positively correlated with EH and TH, and CF was positively correlated with CP, but CT was negatively correlated with CP. Two hundred and fifty-six QTL for correlated traits were detected by multiple traits analysis and 131 new QTL were detected. QTL for several related traits, showing pleiotroy or tight linkage, have been found on more than one chromosome.
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