cultivar identification ( Kimura et al., 2002 ), genetic diversity studies ( Bao et al., 2007 ), and quantitative trait locus mapping ( Perchepied et al., 2015 ; Yamamoto et al., 2014 ). Compared with other molecular markers, SSR markers provide a number
Shuang Jiang, Haishan An, Xiaoqing Wang, Chunhui Shi, Jun Luo, and Yuanwen Teng
Christina H. Hagerty, Alfonso Cuesta-Marcos, Perry Cregan, Qijian Song, Phil McClean, and James R. Myers
Snap bean (Phaseolus vulgaris L.) breeding programs are tasked with developing cultivars that meet the standards of the vegetable processing industry and ultimately that of the consumer, all the while matching or exceeding the field performance of existing cultivars. While traditional breeding methods have had a long history of meeting these requirements, genetic marker technology, combined with the knowledge of important quantitative trait loci (QTL), can accelerate breeding efforts. In contrast to dry bean, snap bean immature pods and seeds are consumed as a vegetable. Several pod traits are important in snap bean including: reduced pod wall fiber, absence of pod suture strings, and thickened, succulent pod walls. In addition, snap bean pods are selected for round pod cross section, and pods tend to be longer with cylindrical seed shape. Seed color is an important trait in snap bean, especially those used for processing, as processors prefer white-seeded cultivars. The objective of this study was to investigate the genetic control of traits important to snap bean producers and processors. RR6950, a small seeded brown indeterminate type IIIA dry bean accession, was crossed to the Oregon State University (OSU) breeding line OSU5446, a type I Blue Lake four-sieve breeding line to produce the RR138 F4:6 recombinant inbred (RI) mapping population. We evaluated the RR138 RI population for processing and morphological traits, especially those affecting pods. The RR138 population was genotyped with the BARCBean6K_3 Beadchip, and single nucleotide polymorphisms (SNPs) were used to assemble a linkage map, and identify QTL for pod traits. The linkage map produced from this study contained 1689 SNPs across 1196cM. The map was populated with an average of one SNP per 1.4 cM, spanning 11 linkage groups. Seed and flower color genes B and P were located on Pv02 and Pv07, respectively. A QTL for string:pod length (PL) ratio was found on Pv02 controlling 32% of total genetic variation. QTL for a suite of important processing traits including pod wall fiber, pod height, pod width, and pod wall thickness were found clustering on Pv04 and controlled 21%, 26%, 18%, and 16% of genetic variation for each of these respective traits. A QTL for PL was found on Pv09 controlling 5% of genetic variation.
I. Paran, I.L. Goldman, and D. Zamir
Quantitative trait loci influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato (Lycopersicon esculentum) with a related wild species (L. cheesmanii). One-hundred-thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 RIL families. Morphological traits, including plant height, fresh weight, node number, first flower-bearing node, leaf length at nodes three and four, and number of branches, were measured in replicated trials during 1991, 1992, and 1993. Significant (P ≤ 0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. Lower plant height, more branches, and shorter internode length were generally associated with RFLP alleles from the L. cheesmanii parent. QTL with large effects on a majority of the morphological traits measured were detected at chromosomes 2, 3, and 4. Large additive effects were measured at significant marker loci for many of the traits measured. Several marker loci exhibited significant associations with numerous morphological traits, suggesting their possible linkage to genes controlling growth and development processes in Lycopersicon.
James W. Olmstead, Hilda Patricia Rodríguez Armenta, and Paul M. Lyrene
Because of financial and labor concerns, growers are interested in using machine harvesting for fruit destined to be fresh marketed. Machine harvest of highbush blueberry (Vaccinium corymbosum) has typically been used to obtain large volumes of fruit destined for processing. Bush architecture, easy detachment of mature berries compared with immature berries, loose fruit clusters, small stem scar, firm fruit, and a concentrated ripening period are breeding goals to develop cultivars amenable to machine harvest. In the University of Florida (UF) southern highbush blueberry [SHB (Vaccinium corymbosum hybrids)] breeding program, sparkleberry (Vaccinium arboreum) has been used in wide crosses in an attempt to introgress traits that may be valuable for machine harvesting, namely upright growth habit with a narrow crown and long flower and fruit pedicels creating loose fruit clusters. Two eras of sparkleberry hybridization experiments have occurred since the early 1980s. The first era used darrow’s evergreen blueberry (Vaccinium darrowii) as a bridge between sparkleberry and tetraploid SHB, with the recently released cultivar FL 01-173 (sold under the trademarked name Meadowlark) as an example of the end product. The second era has used chromosome doubling to develop polyploid sparkleberry selections that were directly crossed with tetraploid SHB. After 1 year of evaluation, a SHB × (SHB × sparkleberry) population developed for linkage and quantitative trait locus mapping showed abundant variation for length:width ratio of the plant, but similarity to the highbush phenotype for peduncle and pedicel length of the fruit. These first evaluations indicate evidence of introgression and provide an initial step toward improved cultivars for mechanical harvesting.
Carlos A. F. Santos and Philipp W. Simon
Markers were placed on linkage groups, ordered, and merged for two unrelated F2 populations of carrot (Daucus carota L.). Included were 277 and 242 dominant Amplified fragment-length polymorphism (AFLP) markers and 10 and eight codominant markers assigned to the nine linkage groups of Brasilia × HCM and B493 × QAL F2 populations, respectively. The merged linkage groups were based on two codominant markers and 28 conserved dominant AFLP markers (based upon sequence and size) shared by both populations. The average marker spacing was 4.8 to 5.5 cM in the four parental coupling phase maps. The average marker spacing in the six merged linkage groups was 3.75 cM with maximum gaps among linkage groups ranging from 8.0 to 19.8 cM. Gaps of a similar size were observed with the linkage coupling phase maps of the parents, indicating that linkage group integration did not double the bias which comes with repulsion phase mapping. Three out of nine linkage groups of carrot were not merged due to the absence of common markers. The six merged linkage groups incorporated similar numbers of AFLP fragments from the four parents, further indicating no significant increase in bias expected with repulsion phase linkage. While other studies have merged linkage maps with shared AFLPs of similar size, this is the first report to use shared AFLPs with highly conserved sequence to merge linkage maps in carrot. The genome coverage in this study is suitable to apply quantitative trait locus analysis and to construct a cross-validated consensus map of carrot, which is an important step toward an integrated map of carrot.
Xiaoying Li, Hongxia Xu, Jianjun Feng, and Junwei Chen
Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotrya japonica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus ×domestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, ≈12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.
Gennaro Fazio, Yizhen Wan, Dariusz Kviklys, Leticia Romero, Richard Adams, David Strickland, and Terence Robinson
The ability of certain apple rootstocks to dwarf their scions has been known for centuries and their use revolutionized apple (Malus ×domestica) production systems. In this investigation, several apple rootstock breeding populations, planted in multiple replicated field and pot experiments, were used to ascertain the degree of dwarfing when grafted with multiple scions. A previous genetic map of a breeding population derived from parents ‘Ottawa 3’ (O.3) and ‘Robusta 5’ (R5) was used for quantitative trait locus (QTL) analysis of traits related to scion vigor suppression, induction of early bearing, and other tree size measurements on own-rooted and grafted trees. The analysis confirmed a previously reported QTL that imparts vigor control [Dw1, log of odds (LOD) = 7.2] on linkage group (LG) 5 and a new QTL named Dw2 (LOD = 6.4) on LG11 that has a similar effect on vigor. The data from this population were used to study the interaction of these two loci. To validate these findings, a new genetic map comprised of 1841 single-nucleotide polymorphisms was constructed from a cross of the dwarfing, precocious rootstocks ‘Geneva 935’ (G.935) and ‘Budagovsky 9’ (B.9), resulting in the confirmation and modeling of the effect of Dw1 and Dw2 on vigor control of apple scions. Flower density and fruit yield data allowed the identification of genetic factors Eb1 (LOD = 7.1) and Eb2 (LOD = 7.6) that cause early bearing of scions, roughly colocated with the dwarfing factors. The major QTL for mean number of fruit produced per tree colocated with Dw2 (LOD = 7.0) and a minor QTL was located on LG16 (LOD = 3.5). These findings will aid the development of a marker-assisted breeding strategy, and the discovery of additional sources for dwarfing and predictive modeling of new apple rootstocks in the Geneva® apple rootstock breeding program.
Haofeng Chen, Vanessa E.T.M. Ashworth, Shizhong Xu, and Michael T. Clegg
The authors report a quantitative genetic analysis of avocado (Persea americana Mill.) growth rate, flower abundance, and fruit set. The data are based on a total of 204 different genotypes of progeny of ‘Gwen’ avocado. Each was replicated four times, with two replicates planted in each of two locations in southern California (Irvine and Riverside). Data were collected over 4 years (consecutive) on tree height, canopy diameter, and trunk diameter, representing three distinct measures of growth rate. Growth data were found to fit a linear regression over years, so the slope (growth rate) was used in the analyses. In addition, 2 years of data on flower abundance and 1 year on fruit set were also collected. Quantitative genetic analyses of these data showed that broad-sense heritability (H) was 35.5%, 30.3%, and 26.6% for tree height, canopy diameter, and trunk diameter respectively; and 33.8% and 23.0% for flowering abundance and fruit set respectively. No genotype-by-location effect was noted for growth rate; however, flower abundance and fruit set showed a relatively weak genotype-by-location effect (21.9% and 17.1% respectively). The H estimates are low, probably as a result of sources of uncontrolled environmental error associated with variation in initial planting dates, but fall within the range that should permit quantitative trait locus analyses. The authors also found a moderate positive correlation between tree growth rates and fruit set, but none between growth rates and flower abundance. Different pollen parents have significantly different impacts on tree growth rates, flower abundance, and fruit set.
Thierry Pascal, Fred Pfeiffer, and Jocelyne Kervella
that in P. davidiana , the quantitative trait locus (QTL) with the strongest effect for powdery mildew resistance, was on this linkage group ( Foulongne et al., 2003a , 2003b ). Vr2 would thus be located on a linkage group distinct from the major
Yonghong Guo, Matthew Kramer, and Margaret Pooler
Stegmeir et al. (2014) explained the inheritance of resistance from P. canescens using a two-gene model and identified a quantitative trait locus associated with resistance from this source. These results readily explain the differences in resistance