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Genetic Background, Inbreeding, and Genetic Uniformity in the National Citrus Breeding Program, Japan

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The Horticulture Journal 86 (2): 200–207. 2017. e Japanese Society for doi: 10.2503/hortj.OKD-013 JSHS Horticultural Science http://www.jshs.jp/ Genetic Background, Inbreeding, and Genetic Uniformity in the National Citrus Breeding Program, Japan Atsushi Imai1,2,3, Takeshi Kuniga1,4, Terutaka Yoshioka1,5, Keisuke Nonaka1,5, Nobuhito Mitani1,2, Hiroshi Fukamachi1,5, Naofumi Hiehata1,6, Masashi Yamamoto1,7 and Takeshi Hayashi3,8* 1Kuchinotsu Citrus Research Station, NARO Institute of Fruit Tree Science, Minamishimabara 859-2501, Japan 2NARO Institute of Fruit Tree and Tea Science, Tsukuba 305-8605, Japan 3Graduate School of Life and Environmental Sciences, Tsukuba University, Tsukuba 305-8666, Japan 4NARO Western Region Agricultural Research Center, Zentsuji 765-0053, Japan 5NARO Institute of Fruit Tree and Tea Science, Shimizu 424-0292, Japan 6Kenou Development Bureau, Nagasaki Prefectural Government, Isahaya 854-0071, Japan 7Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan 8NARO Institute of Crop Science, Tsukuba 305-8518, Japan We analyzed the pedigree records (1995–2010) of the Kuchinotsu Citrus Breeding Program (KCBP) at the National Institute of Fruit Tree Science (NIFTS) in Japan, abbreviated as NIFTS-KCBP, to reveal the genetic background and current status of inbreeding and genetic uniformity of the parental cultivars/genotypes and their F1 breeding progenies. The founding genotypes mostly used for crossing in NIFTS-KCBP were satsuma mandarin (Citrus unshiu Marcow.), sweet orange (C. sinensis [L.] Osbeck), king mandarin (C. nobilis Lour.), clementine (C. clementina hort. ex Tanaka), mediterranean mandarin (C. deliciosa Ten.), dancy tangerine (C. tangerina hort. ex Tanaka), and ponkan (C. reticulata Blanco). The intensive use of these seven genotypes and their progenies as crossed parents has led to a high degree of inbreeding in the breeding population. Moreover, these seven genotypes have dominated about 80% of the genetic composition of the breeding population. Although further studies are needed to reveal the influence of inbreeding and genetic uniformity on agronomically important traits, these data offer useful information for the selection of cross combinations and breeding strategies in the ongoing NIFTS citrus breeding program, Japan. Key Words: citrus hybrids, founding genotypes, inbreeding coefficients, pedigree, plant breeding. genotypes and their progenies can lead to inbreeding Introduction depression and genetic uniformity in breeding materi- Inbreeding and genetic uniformity in breeding popu- als, resulting in the loss of breeding efficiency in the lations are major concerns for crop breeders. In most long term. Inbreeding depression downgrades fitness- fruit breeding programs, the number of high-quality related traits, such as tree vigor, whereas genetic uni- genotypes is restricted, and thus they are extensively formity causes genetic erosion and decreases the used as crossed parents (Kajiura and Sato, 1990; Noiton genetic gain per selection. Therefore, both inbreeding and Alspach, 1996; Scorza et al., 1985). The common and genetic uniformity prohibit the future progress in practice of using a limited number of genotypes with genetic performance. For the continuous development high quality as crossed parents contributes to the effi- of improved cultivars that meet market demands, the cient genetic improvement in the initial stages of a current status of inbreeding and genetic uniformity in breeding program. However, the recurrent use of few the existing breeding populations needs to be evaluated. Several studies have evaluated the inbreeding and genetic uniformity in breeding populations of fruit tree Received; May 2, 2016. Accepted; August 16, 2016. First Published Online in J-STAGE on September 24, 2016. crops. For instance, Kajiura and Sato (1990) reported * Corresponding author (E-mail: [email protected]). that only 15 cultivars out of the 1212 native varieties © 2017 The Japanese Society for Horticultural Science (JSHS), All rights reserved. Hort. J. 86 (2): 200–207. 2017. 201 are used as crossed parents in Japanese pear breeding; Genetic background Scorza et al. (1985) demonstrated that the selection for The pedigree records of 126 parental cultivars and fruit quality in the freestone peach has led to a high de- their 12541 F1 breeding progenies that contained the gree of inbreeding and genetic uniformity in the eastern names of individual genotypes and their seed and pollen United States; and Yamada (1993) and Yamada et al. parents were obtained from NIFTS-KCBP. The pedi- (1994) found that repeated crosses over generations grees of all genotypes were traced back to genotypes within the narrow gene pool of persimmon have led to with unknown parents, which were regarded as found- inbreeding depression, which reduces tree vigor, pro- ing genotypes, and all the founding genotypes and an- ductivity, and fruit weight. cestral genotypes were added to the pedigree records to In Japan, the National Citrus Breeding Program is obtain the full pedigree charts that were constructed conducted at the National Institute of Fruit Tree Science using Pedimap (Voorrips et al., 2012). Such full pedi- (NIFTS) Kuchinotsu Citrus Research Station and gree information was used to reveal the genetic back- NIFTS Okitsu Citrus Research Station. The Kuchinotsu ground and founding genotypes of the parental cultivars Citrus Breeding Program (KCBP) at the NIFTS, which and their F1 progenies. is abbreviated as NIFTS-KCBP, started in 1964 and has been recognized as one of the largest fruit breeding pro- Inbreeding and genetic uniformity grams in the world (Matsumoto and Takahara, unpub- The inbreeding coefficients of 126 parental cultivars lished). NIFTS-KCBP has successfully developed 21 and their 12541 F1 progenies, as well as the coefficients novel citrus cultivars such as ‘Shiranuhi’ (Matsumoto, of co-ancestry between them and their founding geno- 2001) and ‘Setoka’ (Matsumoto et al., 2003), which are types, were computed based on the assumption that the widely grown in Japan. founding genotypes were genetically unrelated and non- Since the 1970s, fruit quality traits, including high inbred. The inbreeding coefficient was defined as the sugar content, easy peeling, seedlessness, soft pulp probability that two alleles of an individual at a given firmness, and soft segment firmness, have been the locus were identical by descent (IBD) and reflected the main breeding targets of NIFTS-KCBP. These breeding genetic similarity of a mating pair to generate the indi- objectives narrowed down the candidate parental culti- vidual. To investigate the changes in the inbreeding co- vars, and thus may lead to inbreeding depression and efficients of F1 progenies, we evaluated the mean genetic uniformity in the breeding populations. How- inbreeding coefficients of F1 progenies obtained in each ever, the genetic background, as well as the degree of year from 1995 through 2010. Coefficient of co- inbreeding and genetic uniformity in NIFTS-KCBP ancestry between two individuals was defined as the populations, have not yet been investigated. probability that the two alleles sampled from respective The objectives of this study were to reveal the genet- individuals at a given locus were IBD. Thus, the coeffi- ic background and current status of inbreeding and cients of co-ancestry between parental cultivars or F1 genetic uniformity in NIFTS-KCBP parental cultivars/ progenies and the founding genotypes reflected the ge- genotypes (hereinafter referred to as parental cultivars) nome composition of a breeding population, each com- and their F1 breeding progenies using their pedigree in- ponent of which was originated from the genomes of formation. These estimates can offer useful information the founding genotypes. We calculated twice the coeffi- for the future selection of parental cultivars or plants for cient of co-ancestry as a numerator relationship coeffi- cross combinations and breeding strategies. cient between the parental cultivars or F1 progenies and the founding genotypes, which can be interpreted as the Materials and Methods genetic contributions of founding genotypes to individ- Plant materials uals in a breeding population (Bulmer, 1980). Parental cultivars and their F1 breeding progenies ob- Inbreeding coefficients and coefficients of co- tained in NIFTS-KCBP from 1995 to 2010 were con- ancestry were calculated using Peditree (van Berloo and sidered in this study. Seventy-three seed parents and 69 Hutten, 2005) based on the assumption that the found- pollen parents, a total of 126 parental cultivars, pro- ing genotypes were unrelated and non-inbred, and that duced 12541 F1 progenies from 466 cross combinations breeding selections had no influence on the genetic con- in NIFTS-KCBP during the period. About 1000 F1 tribution of descendant genotypes. In addition, all mu- progenies from 20–40 cross combinations were planted tants included in the breeding population were regarded in breeding fields in each year from 1995 through 2010. to have the same genetic composition as the original From these 12541 F1 progenies, we selected a promi- genotypes. nent early-maturated cultivar ‘Mihaya’ (Nonaka et al., Results 2012), and two prominent genotypes were selected and are evaluated in a national trial as of June 2016. They Genetic background were also used as parental cultivars, and were included The pedigree chart of 126 parental cultivars used for in the 126 parental cultivars in this study. crossing between 1995 and
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  • MITE Insertion-Dependent Expression of Citrkd1 with a RWP-RK Domain

    MITE Insertion-Dependent Expression of Citrkd1 with a RWP-RK Domain

    Shimada et al. BMC Plant Biology (2018) 18:166 https://doi.org/10.1186/s12870-018-1369-3 RESEARCH ARTICLE Open Access MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues Takehiko Shimada1*, Tomoko Endo1, Hiroshi Fujii1, Michiharu Nakano2, Aiko Sugiyama2, Genya Daido2, Satoshi Ohta1, Terutaka Yoshioka1 and Mitsuo Omura2* Abstract Background: Somatic embryogenesis in nucellar tissues is widely recognized to induce polyembryony in major citrus varieties such as sweet oranges, satsuma mandarins and lemons. This capability for apomixis is attractive in agricultural production systems using hybrid seeds, and many studies have been performed to elucidate the molecular mechanisms of various types of apomixis. To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between monoembryonic and polyembryonic varieties. The full length of CitRKD1, which was identified as a candidate gene responsible for citrus somatic embryogenesis, was isolated from satsuma mandarin and its molecular function was investigated using transgenic ‘Hamlin’ sweet orange by antisense-overexpression. Results: The candidate gene CitRKD1, predominantly transcribed in reproductive tissues of polyembryonic varieties, is a member of the plant RWP-RK domain-containing protein. CitRKD1 of satsuma mandarin comprised two alleles (CitRKD1-mg1 and CitRKD1-mg2) at the polyembryonic locus controlling embryonic type (mono/polyembryony) that were structurally divided into two types with or without a miniature inverted-repeat transposable element (MITE)- like insertion in the upstream region. CitRKD1-mg2 with the MITE insertion was the predominant transcript in flowers and young fruits where somatic embryogenesis of nucellar cells occurred.