Mapping of Nematode Resistance in Hexaploid Sweetpotato Using an Next-Generation Sequencing-Based Association Study

The southern root-knot nematode (SRKN; Meloidogyne incognita) is a typical parasitic nematode that affects sweetpotato [Ipomoea batatas (L.) Lam.], causing a significant decrease in crop yield and commercial value. In Japan, the SRKN is classified into 10 races: SP1-SP5, SP6-1, SP6-2, and SP7-SP9, with the dominant race differing according to the cultivation area. Soil insecticides have previously been used to reduce the soil density of SRKNs; however, this practice is both costly and labor intensive. Therefore, the development of SRKN-resistant sweetpotato lines and cultivars is necessary. However, due to the complexity of polyploid inheritance and the highly heterogeneous genomic composition of sweetpotato, genetic information and research for this species are significantly lacking compared to those for other major diploid crop species. In this study, we utilized the recently developed genome-wide association approach, which uses multiple-dose markers to assess autopolyploid species. We performed an association analysis to investigate resistance toward SRKN-SP2, which is the major race in areas with high sweetpotato production in Japan. The segregation ratio of resistant and susceptible lines in the F-1 mapping population derived from the resistant "J-Red" and susceptible "Choshu" cultivars was fitted to 1: 3, suggesting that resistance to SP2 may be regulated by two loci present in the simplex. By aligning the double digest restriction-site associated DNA sequencing reads to the published Ipomoea trifida reference sequence, 46,982 single nucleotide polymorphisms (SNPs) were identified (sequencing depth > 200). The association study yielded its highest peak on chromosome 7 (Chr07) and second highest peak on chromosome 3 (Chr03), presenting as a single-dose in both loci. Selective DNA markers were developed to screen for resistant plants using the SNPs identified on Chr03 and Chr07. Our results showed that SRKN-SP2-resistant plants were selected with a probability of approximately 70% when combining the two selective DNA markers. This study serves as a model for the identification of genomic regions that control agricultural traits and the elucidation of their effects, and is expected to greatly advance marker-assisted breeding and association studies in polyploid crop species

Issues in Student Surveys of a Permanent Experimental Stand in a Research Forest

学生実習による固定試験地調査を通じて，授業でのフィールド調査の割り当て方法について検討した。信州大学農学部手良沢山演習林のイチイ植林地において，参加学生20名を4班に分け，先回り探索（他の班との位置関係と未調査木の位置をもとに次の調査木を選ばせる方式）で，立木のサイズと位置の計測を実施した。全体では94本（班ごとに17～28本）の立木が調査され，胸高直径（DBH）は正規分布し，班ごとに見ても平均DBHに有意差はなく概ね正規分布していた。立木の位置情報をもとに調査中の各班の移動の軌跡を描いたところ，調査終了まで開始時点の各班の位置関係がほぼ保たれ，軌跡が互いに交錯することはなかった。また，班ごとで調査終了までの時間差はほとんど生じなかった。次の調査木への距離（平均の水平距離3.0～3.5m，垂直距離1.0～1.8m）に班ごとに有意差はなく，調査条件に班ごとの著しい違いはなかった。また，最も調査本数の多かった班で，標識番号の誤記入が1件見られ，それによって欠測と重複カウントをそれぞれ1本ずつ生じたのと等しい状況になった。各班の意思に任せる先回り方式での調査割り当てでは，班ごとの能率に合わせて調査地が分担されることが確かめられたが，問題点として調査ミスを検出しにくいことが挙げられた。Article環境科学年報 40:57-63(2018)research repor

Polyploid GWAS reveals the basis of molecular marker development for complex breeding traits including starch content in the storage roots of sweet potato

Given the importance of prioritizing genome-based breeding of sweet potato to enable the promotion of food and nutritional security for future human societies, here, we aimed to dissect the genetic basis of storage root starch content (SC) when associated with a complex set of breeding traits including dry matter (DM) rate, storage root fresh weight (SRFW), and anthocyanin (AN) content in a mapping population containing purple-fleshed sweet potato. A polyploid genome-wide association study (GWAS) was extensively exploited using 90,222 single-nucleotide polymorphisms (SNPs) obtained from a bi-parental 204 F1 population between ‘Konaishin’ (having high SC but no AN) and ‘Akemurasaki’ (having high AN content but moderate SC). Through the comparison of polyploid GWAS on the whole set of the 204 F1, 93 high-AN-containing F1, and 111 low-AN-containing F1 populations, a total of two (consists of six SNPs), two (14 SNPs), four (eight SNPs), and nine (214 SNPs) significantly associated signals were identified for the variations of SC, DM, SRFW, and the relative AN content, respectively. Of them, a novel signal associated with SC, which was most consistent in 2019 and 2020 in both the 204 F1 and 111 low-AN-containing F1 populations, was identified in homologous group 15. The five SNP markers associated with homologous group 15 could affect SC improvement with a degree of positive effect (~4.33) and screen high-starch-containing lines with higher efficiency (~68%). In a database search of 62 genes involved in starch metabolism, five genes including enzyme genes granule-bound starch synthase I (IbGBSSI), α-amylase 1D, α-amylase 1E, and α-amylase 3, and one transporter gene ATP/ADP-transporter were located on homologous group 15. In an extensive qRT-PCR of these genes using the storage roots harvested at 2, 3, and 4 months after field transplantation in 2022, IbGBSSI, which encodes the starch synthase isozyme that catalyzes the biosynthesis of amylose molecule, was most consistently elevated during starch accumulation in sweet potato. These results would enhance our understanding of the underlying genetic basis of a complex set of breeding traits in the starchy roots of sweet potato, and the molecular information, particularly for SC, would be a potential platform for molecular marker development for this trait

Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato

The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (similar to 3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F-1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F-1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita

路網配置, 架線配置, 原木輸送に関連する森林作業計画のモデル化とシミュレーション

京都大学0048新制・課程博士博士(農学)甲第18321号農博第2046号新制||農||1021(附属図書館)学位論文||H26||N4828(農学部図書室)31179京都大学大学院農学研究科森林科学専攻(主査)教授 吉岡 崇仁, 教授 德地 直子, 准教授 長谷川 尚史学位規則第4条第1項該当Doctor of Agricultural ScienceKyoto UniversityDFA

Annual Availability of Forest Biomass Resources for Woody Biomass Power Generation Plants from Subcompartments and Aggregated Forests in Tohoku Region of Japan

To utilize timber and forest biomass resources for bioenergy, technically feasible and economically viable timber and forest biomass resources should be estimated accurately considering their long-term availability. This study focuses on five prefectures, namely, Aomori, Iwate, Miyagi, Akita, and Yamagata, and considers trade between these prefectures. The annual availability of timber and forest biomass resources, such as small-diameter or defect stem logs, rather than logging residues in Japan was estimated as supply potential from profitable forests where expected revenues surpassed all costs, from planting to final harvest. As a result, the supply potential and annual availability of timber were estimated at 11,388,960 m3/year and 1,631,624 m3/year, whereas those of forest biomass resources were estimated at 2,277,792 m3/year and 326,325 m3/year, respectively. Therefore, the rate of annual availability to supply potential was 14.3%. Since timber production and wood chip usage from thinned woods and logging residues in 2018 were 4,667,000 m3/year and 889,600 m3/year, the rates of annual availability for timber and forest biomass resources to those values were 35.0% and 36.7%, respectively. Furthermore, the demand was estimated at 951,740 m3/year from 100,000 m3/year with a generation capacity of 5 MW. The rate of forest biomass resource availability to demand was 34.2%. A thinning subsidy was provided for operational site areas larger than 5 ha in Japan. The rates from subcompartments and aggregated forests with a thinning subsidy increased to 91.4% and 190.3%, respectively. Thus, the estimated availability from aggregated forests with a thinning subsidy met the demand sufficiently in this region

Supply Potential and Annual Availability of Timber and Forest Biomass Resources for Energy in Japan

This study calculated incomes and expenditures such as silvicultural and harvesting as well as stumpage prices on Japanese cedar, cypress, pine, and larch forests using the silvicultural prescriptions set based on the regional forest plans and operation systems set based on topographic conditions such as slope angles and height differences with GIS. Then, this study estimated the availability of unused materials for woody biomass power generation plants under operation with FIT at the end of June 2020 as the supply potential from the profitable subcompartments. Considering the subsidy rate of 100% to secure the reforestations, the availabilities met the demands in Japan as a whole