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Lin Zhou, Qianqian Shi, Yan Wang, Kui Li, Baoqiang Zheng, and Kun Miao

reference genes were identified based on our previous trancriptome analysis, including six traditional housekeeping genes, ACT2 , GAPDH , TUA , EF1α , TUB , and UBQ and six newly identified candidate reference genes, CYP , EIF5A , helicase , PP2A

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Yiwei Jiang, Eric Watkins, Shuwei Liu, Xiaoqing Yu, and Na Luo

candidate genes is essential for elucidating molecular adaptations of grass plants to drought stress. Furthermore, key candidate genes associated with drought tolerance can be used for improving drought tolerance of turfgrass through marker

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Geoffrey Meru and Cecilia McGregor

step toward developing such genomic tools for watermelon, the current study aimed to identify genetic loci and candidate genes associated with fatty acid composition in watermelon seed for future application in MAS for improved oil quality. To our

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Li Huang, Wan-zhi Ye, Ting-ting Liu, and Jia-shu Cao

of multiple nuclear genes potentially can develop into stable genic male-sterile lines. For this reason, isolation of the candidate genes imparting genic male sterility and knowledge of the effects of these genes are important for the understanding of

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Yu Bai, Ying Zhou, Xiaoqing Tang, Yu Wang, Fangquan Wang, and Jie Yang

candidate genes related to the flowering pathway were analyzed by quantitative real time polymerase chain reaction (qRT-PCR). The results of this study will enhance our understanding of the bolting and flowering-time regulatory networks in I. indigotica

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Verónica Raga, Guillermo P. Bernet, Emilio A. Carbonell, and Maria J. Asins

affect numerous citrus attributes ( Castle, 2010 ) making interpretation of data analysis very complicated. An alternative strategy is the analysis of candidate genes functionally involved in the salt tolerance response. These genes could serve as useful

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Cameron P. Peace, Carlos H. Crisosto, Fredrick A. Bliss, and Thomas M. Gradziel

Candidate gene (CG) analysis can be an efficient approach for identifying genes controlling important traits in fruit production. Three chronological steps have been described for determining candidate genes for a trait—proposing, screening, and validating—and we have applied these to the problem of internal breakdown of peach and nectarine. Internal breakdown (IB), also known as chilling injury, is the collective term for various disorders that occur during prolonged cold storage and/or after subsequent ripening of stone fruit. Symptoms include mealiness, browning, and bleeding. Candidate genes for IB symptoms were proposed based on knowledge of the biochemical or physiological pathways leading to phenotypic expression of the traits. Gene sequences for proposed CGs were obtained primarily from the Genome Database for Rosaceae. Screening the CGs involved identifying polymorphism within a progeny population, relying mainly on simple PCR tests. Several polymorphic CGs were located on a peach linkage map and compared with phenotypic variation for IB susceptibility. A major QTL for mealiness coincided with the Freestone-Melting flesh locus, which itself is likely to be controlled by a CG encoding endopolygalacturonase, an enzyme involved in pectin degradation. Further gene sequences positioned on the consensus linkage map of Prunus by other researchers were co-located with QTLs for IB traits. Validation of the role of identified CGs will require detailed physiological or transgenic studies.

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Douglas G. Bielenberg, Ying Wang, Gregory L. Reighard, and Albert G. Abbott

`Evergrowing' (evg) peach is a naturally occurring mutant unable to enter winter dormancy in response to dormancy inducing conditions. The evg mutant is one of only two described mutants affecting winter dormancy in woody perennial trees. The evg mutation segregates as a single recessive gene and previous work by our group has fine mapped the trait between flanking markers separated by 3.3 centiMorgans. This region was physically mapped using a bacterial artificial chromosome (BAC) library from and a contig of overlapping genomic fragments identified. We have utilized several approaches to complete the sequencing of a 132 kilobase region of the peach genome derived from three overlapping BACs that encompass the complete EVG gene containing region. We present here our analysis and annotation of the genomic region, including putative and experimentally verified gene coding sequences. A primary feature of the region is a large tandem duplication of a region containing a MADS-box type DNA binding transcription factor resulting in six similar copies of the gene, all of which appear to be expressed at the mRNA level in wild-type germplasm. Hybridization analysis revealed the presence of a large deletion in the mutant genome. Five of the identified genes fall within the evg mutation and represent new candidates for the control of entrance into winter dormancy.

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J. Steven Brown, R.J. Schnell, J.C. Motamayor, Uilson Lopes, David N. Kuhn, and James W. Borrone

A genetic linkage map was created from 146 cacao trees (Theobroma cacao), using an F2 population produced by selfing an F1 progeny of the cross Sca6 and ICS1. Simple sequence repeat (SSR) markers (170) were used principally for this map, with 12 candidate genes [eight resistance gene homologues (RGH) and four stress related WRKY genes], for a total of 182 markers. Joinmap software was used to create the map, and 10 linkage groups were clearly obtained, corresponding to the 10 known chromosomes of cacao. Our map encompassed 671.9 cM, approximately 100 cM less than most previously reported cacao maps, and 213.5 cM less than the one reported high-density map. Approximately 27% of the markers showed significant segregation distortion, mapping together in six genomic areas, four of which also showed distortion in other cacao maps. Two quantitative trait loci (QTL) for resistance to witches' broom disease were found, one producing a major effect and one a minor effect, both showing important dominance effects. One QTL for trunk diameter was found at a point 10.2 cM away from the stronger resistance gene. One RGH flanked the minor QTL for witches' broom resistance, implying possible association. QTLs mapped in F2 populations produce estimates of additive and dominance effects, not obtainable in F1 crosses. As dominance was clearly shown in the QTL found in this study, this population merits further study for evaluation of dominance effects for other traits. This F2 cacao population constitutes a useful link for genomic studies between cacao and cotton, its only widely grown agronomic relative.

Open access

Qiuyue Ma, Shushun Li, Jing Wen, Lu Zhu, Kunyuan Yan, Qianzhong Li, Shuxian Li, and Bin Zhang

. truncatum is limited. The first comprehensive study characterizing the gene expression in A. truncatum seeds was conducted by Wang et al. (2018) . They compared the transcriptomes of two genotypes of A. truncatum seeds and identified candidate genes