Browsing by Author "Tao, Aifen"

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High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing
(2017-05) Tao, Aifen; Huang, Long; Wu, Guifen; Keshavarz-Afshar, Reza; Qi, Jianmin; Xu, Jiantang; Fang, Pingping; Lin, Lihui; Zhang, Liwu; Lin, Peiqing
BACKGROUND Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. RESULTS An F8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. \'SNP_only\' markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14-15.63% of the phenotypic variance. CONCLUSIONS To our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.
Variation in Yield, Starch, and Protein of Dry Pea Grown across Montana
(2017-05) Tao, Aifen; Afshar, Reza Keshavarz; Huang, Jinwen; Mohammed, Yesuf Assen; Espe, Matthew; Chen, Chengci
Pea (Pisum sativum L.) has long been an important component of the human diet, providing an excellent source of protein. In addition to its protein, pea starch, especially resistant starch (RS), has received an extensive attention in food industries in recent years. We evaluated nine pea cultivars varying in cotyledon color, grain weight, maturity group, and phenology planted at five locations with diverse climatic conditions across Montana in 2013 and 2014 to assess genetic and environmental factors affecting their yield, protein, RS, and total starch (TS). Grain yield varied from 982 to 5951 kg ha(-1), RS content ranged from 5 to 53 g kg(-1), and protein from 159 to 251 g kg(-1). Statistical analysis showed that environment was the most important driving factor in grain yield, protein, and TS determination whereas RS content was mainly determined by cultivar. Drought at all phenological stages reduced pea yield and different cultivars tended to respond differently. Yield was positively correlated with protein, implying a potential to select/breed a cultivar with higher yield and protein. Protein was negatively correlated with TS, thus protein-or starch-type cultivars may be bred for different end users. Compared to other cultivars tested, DS Admiral was the most promising one with above average yield, protein, and RS.