Development of SSR Markers in Hickory (Carya cathayensis Sarg.) and Their Transferability to Other Species of Carya

Abstract

Hickory (Carya cathayensis Sarg.), an important nut-producing species in Southeastern China, has high economic value, but so far there has been no cultivar bred under species although it is mostly propagated by seeding and some elite individuals have been found. It has been found recently that this species has a certain rate of apomixis and poor knowledge of its genetic background has influenced development of a feasible breeding strategy. Here in this paper we first release SSR (Simple sequence repeat) markers developed in this species and their transferability to other three species of the same genus, Carya. A total of 311 pairs of SSR primers in hickory were developed based on sequenced cDNAs of a fruit development-associated cDNA library and RNA-seq data of developing female floral buds and could be used to distinguish hickory, C. hunanensis Cheng et R. H. Chang ex R. H. Chang et Lu, C. illinoensis K. Koch (pecan) and C. dabieshanensis M. C. Liu et Z. J. Li, but they were monomorphic in both hickory and C. hunanensis although multi-alleles have been identified in all the four species. There is a transferability rate of 63.02% observed between hickory and pecan and the markers can be applied to study genetic diversity of accessions in pecan. When used in C. dabieshanensis, it was revealed that C. dabieshanensis had the number of alleles per locus ranging from 2 to 4, observed heterozygosity from 0 to 0.6667 and expected heterozygosity from 0.333 to 0.8667, respectively, which supports the existence of C. dabieshanensis as a separate species different from hickory and indicates that there is potential for selection and breeding in this species.

Crop Vulnerability: Carya

“…The focus of Chinese efforts has been on C. cathayensis, the foundation of a respected native nut industry centered at Linan, Zhejiang, People's Republic of China. The species has been extensively sequenced and characterized using a variety of molecular methods (Huang et al, 2013;Li et al, 2014;Wang et al, 2011). Apomixis has been reported for the species (Zhang et al, 2012), an observation consistent with the lack of polymorphism in seedling accessions of the species observed over several years in the NCGR-Carya collections (Grauke and Mendoza-Herrera, 2012).…”

“…Whether the collections of Guo et al (2015) included populations of C. dabieshanensis in their genetic evaluations of Anhui Carya populations is unknown. Recent research (Li et al, 2014) comparing neutral genetic diversity between C. cathayensis and C. dabieshanensis imply increased interest in distinguishing and using that germplasm. Grauke and Mendoza-Herrera (2012) reported patterns in maternally inherited plastid profiles that consistently distinguished specimens of C. dabieshanensis from C. cathayensis in limited numbers of observations, but such distinctions also separate geographic populations of pecan that are not recognized by even varietal, much less species status .…”

Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

“…Therefore, these gSSR loci exhibited high polymorphisms in different germplasms and could be used in genetic diversity study, genetic map construction, Quantitative trait loci (QTL) mapping, as well as cultivar identification in pecan. For the cross-transferability of gSSR loci, 86.67% (26/30) of gSSRs can be used in hickory, which was higher than that in a previous study (63.02%) [20]. Moreover, the transferability rates were 83.33% (25/30) and 73.33% (22/30) between pecan and two other Carya species of C. dabieshanensis and C. hunanensis, respectively (Table 4).…”

“…In total, 28 SSRs (including 25 genome SSRs and three chloroplast SSRs) have been development in pecan, and a set of 19 SSR loci have been used in genetic diversity studies [12,13,18,19]. Li et al (2014) developed a set of SSRs based on transcriptome sequences of Chinese hickory (C. cathayensis Sarg.) and identified the cross-transferability to other species of Carya; however, the availability of these markers has not been fully evaluated in pecan [20].…”

“…Li et al (2014) developed a set of SSRs based on transcriptome sequences of Chinese hickory (C. cathayensis Sarg.) and identified the cross-transferability to other species of Carya; however, the availability of these markers has not been fully evaluated in pecan [20]. Recently, 87,446 SNPs have been discovered in pecan individuals by genotyping by sequencing (GBS), and 17 SNPs were significantly associated with the flowering type [14].…”