1
|
Yamasani MR, Pandu VR, Kalluru S, Bommaka RR, Bandela R, Duddu B, Komeri S, Kumbha D, Vemireddy LR. Haplotype analysis of QTLs governing early seedling vigor-related traits under dry-direct-seeded rice (Oryza sativa L.) conditions. Mol Biol Rep 2023; 50:8177-8188. [PMID: 37555871 DOI: 10.1007/s11033-023-08714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial. METHODS AND RESULTS In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2. CONCLUSIONS In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.
Collapse
Affiliation(s)
- Mounika Reddy Yamasani
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Vasanthi Raguru Pandu
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Rupeshkumar Reddy Bommaka
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Ramanamurthy Bandela
- Department of Statistics and Computer Applications, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Bharathi Duddu
- Department of Genetics and Plant Breeding, Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Srikanth Komeri
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Dineshkumar Kumbha
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India.
| |
Collapse
|
2
|
Yamaguchi N, Sato Y, Taguchi-Shiobara F, Yamashita K, Kawasaki M, Ishimoto M, Senda M. A novel QTL associated with tolerance to cold-induced seed cracking in the soybean cultivar Toyomizuki. BREEDING SCIENCE 2023; 73:204-211. [PMID: 37404349 PMCID: PMC10316309 DOI: 10.1270/jsbbs.22066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/25/2022] [Indexed: 07/06/2023]
Abstract
Low temperatures after flowering cause seed cracking (SC) in soybean. Previously, we reported that proanthocyanidin accumulation on the dorsal side of the seed coat, controlled by the I locus, may lead to cracked seeds; and that homozygous IcIc alleles at the I locus confer SC tolerance in the line Toiku 248. To discover new genes related to SC tolerance, we evaluated the physical and genetic mechanisms of SC tolerance in the cultivar Toyomizuki (genotype II). Histological and texture analyses of the seed coat revealed that the ability to maintain hardness and flexibility under low temperature, regardless of proanthocyanidin accumulation in the dorsal seed coat, contributes to SC tolerance in Toyomizuki. This indicated that the SC tolerance mechanism differed between Toyomizuki and Toiku 248. A quantitative trait loci (QTL) analysis of recombinant inbred lines revealed a new, stable QTL related to SC tolerance. The relationship between this new QTL, designated as qCS8-2, and SC tolerance was confirmed in residual heterozygous lines. The distance between qCS8-2 and the previously identified QTL qCS8-1, which is likely the Ic allele, was estimated to be 2-3 Mb, so it will be possible to pyramid these regions to develop new cultivars with increased SC tolerance.
Collapse
Affiliation(s)
- Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Yumi Sato
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Fumio Taguchi-Shiobara
- Institute of Crop Science, The National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuki Yamashita
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Michio Kawasaki
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Masao Ishimoto
- Institute of Crop Science, The National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| |
Collapse
|
3
|
Panja S, Kar RK, Chandra Dey P, Dey N. Underpinning the soft nature of soak-n-eat rice - A physicochemical and molecular approach. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
4
|
Katoch M, Mane RS, Chahota RK. Identification of QTLs Linked to Phenological and Morphological Traits in RILs Population of Horsegram ( Macrotyloma uniflorum). Front Genet 2022; 12:762604. [PMID: 35145543 PMCID: PMC8821879 DOI: 10.3389/fgene.2021.762604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/09/2021] [Indexed: 11/13/2022] Open
Abstract
Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] is an important legume but understudied in terms of its genetic improvement. Genetic information on various phenological and morphological traits may help in the utilization of new genes for breeding in horsegram and thus affect agronomic practices and crop yield. A total of 162 recombinant inbred lines derived from intraspecific crosses between HPKM249 × HPK4 was used to construct a genetic linkage map and to identify quantitative trait loci (QTLs) associated with phenological and morphological traits. Of the total 2011 molecular markers, which were screened on parental lines for polymorphism survey, 493 markers were found to be polymorphic and used for genotyping of recombinant inbred line population. Out of 493 polymorphic markers, 295 were mapped on ten linkage groups at LOD 3.5 spanning a total distance of 1,541.7 cM with an average distance between markers of 5.20 cM. Phenotypic data of two years at two different locations were used to identify QTLs by composite interval mapping A total of four QTLs (LOD ≥2.5) for phenological traits (days to 50% flowering, reproductive period and days to maturity) and seven QTLs (LOD ≥2.5) for morphological traits (plant height, primary branches and secondary branches) were detected across different environments. The phenotypic variation explained by QTLs ranged from 6.36 to 47.53%. The present study will help to augment scanty genomic information in this orphan crop that would provide genomics tools to breeders for its genetic enhancement through molecular-assisted selection.
Collapse
Affiliation(s)
- Megha Katoch
- Department of Agricultural Biotechnology, College of Agriculture, CSK HP Krishi Vishvavidyalaya, Himachal Pradesh, India
| | | | | |
Collapse
|
5
|
Yamaguchi N, Taguchi-Shiobara F, Sato Y, Senda M, Ishimoto M, Kousaka F. Identification and validation of quantitative trait loci associated with seed yield in soybean. BREEDING SCIENCE 2021; 71:396-403. [PMID: 34776747 PMCID: PMC8573547 DOI: 10.1270/jsbbs.20153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/03/2021] [Indexed: 06/13/2023]
Abstract
In soybean [Glycine max (L.) Merrill], the genetic analysis of seed yield is important to aid in the breeding of high-yielding cultivars. Seed yield is a complex trait, and the number of quantitative trait loci (QTL) involved in seed yield is high. The aims of this study were to identify QTL associated with seed yield and validate their effects on seed yield using near-isogenic lines. The QTL analysis was conducted using a recombinant inbred line population derived from a cross between Japanese cultivars 'Toyoharuka' and 'Toyomusume', and eight seed yield-associated QTL were identified. There were significant positive correlations between seed yield and the number of favorable alleles at QTL associated with seed yield in the recombinant inbred lines for three years. The effects of qSY8-1, a QTL promoting greater seed yield, was validated in the Toyoharuka background. In a two-year yield trial, the 100-seed weight and seed yield of Toyoharuka-NIL, the near-isogenic line having the Toyomusume allele at qSY8-1, were significantly greater than those of Toyoharuka (106% and 107%, respectively) without any change for days to flowering and maturity. Our results suggest that qSY8-1 was not associated with maturity genes, and contributed to the 100-seed weight.
Collapse
Affiliation(s)
- Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Fumio Taguchi-Shiobara
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yumi Sato
- Faculty of Agriculture and Life Sciences, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mineo Senda
- Faculty of Agriculture and Life Sciences, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Masao Ishimoto
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fumiko Kousaka
- Hokkaido Research Organization Central Agricultural Experiment Station, Higashi 6 sen Kita 15 Gou, Naganuma-cho, Yubari-gun, Hokkaido 069-1395, Japan
| |
Collapse
|
6
|
Kato S, Yokota Y, Suzuki R, Fujisawa Y, Sayama T, Kaga A, Anai T, Komatsu K, Oki N, Kikuchi A, Ishimoto M. Identification of a cytochrome P450 hydroxylase, CYP81E22, as a causative gene for the high sensitivity of soybean to herbicide bentazon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2105-2115. [PMID: 32200415 DOI: 10.1007/s00122-020-03580-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE A frame shift invoked by a single-base deletion in the gene encoding a cytochrome P450 hydroxylase, CYP81E22, causes the loss of bentazon detoxification function in soybean. Bentazon is an effective herbicide in soybean cultivation applied at post-emergence stages for control of several broadleaf weeds. However, some soybean cultivars are highly sensitive to bentazon and are killed upon application. In this study, the gene related to the high sensitivity of soybean cultivars to bentazon was mapped to chromosome 16, and its location was narrowed down to a 257-kb region where three cytochrome P450 genes were located. In these genes, a single-base deletion of cytosine was detected in the coding region of Glyma.16G149300, CYP81E22, at + 1465 bp downstream from the translation start codon, leading to a frame shift in the open reading frame and creating a premature stop codon. This stop codon resulted in the loss of more than half of the P450, and consequently, the remaining molecule failed to form a functioning protein. This single-base deletion was common among the highly sensitive cultivars screened from the soybean mini-core collection and other previously reported highly sensitive cultivars. Furthermore, we screened plant lines from the targeting-induced local lesions in genomes library of the soybean cultivar Enrei based on a modelled 3D structure of CYP81E22. The lines with mutations in Glyma.16G149300 were highly sensitive to bentazon, which provides strong evidence that Glyma.16G149300 is the gene responsible for high sensitivity to bentazon.
Collapse
Affiliation(s)
- Shin Kato
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 297 Uenodai, Kariwano, Daisen, Akita, 019-2112, Japan
| | - Yuko Yokota
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Rintaro Suzuki
- Advanced Analysis Center, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yukiko Fujisawa
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takashi Sayama
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Western Region Agricultural Research Center, NARO, 1-3-1 Senyu-cho, Zentsuji, Kagawa, 765-8508, Japan
| | - Akito Kaga
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga, 840-8502, Japan
| | - Kunihiko Komatsu
- Western Region Agricultural Research Center, NARO, 1-3-1 Senyu-cho, Zentsuji, Kagawa, 765-8508, Japan
| | - Nobuhiko Oki
- Kyushu Okinawa Agricultural Research Center, NARO, 2421 Suya, Koshi, Kumamoto, 861-1192, Japan
| | - Akio Kikuchi
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 297 Uenodai, Kariwano, Daisen, Akita, 019-2112, Japan
| | - Masao Ishimoto
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| |
Collapse
|
7
|
Identification of genomic regions associated with early plant vigour in lentil (Lens culinaris). J Genet 2020. [DOI: 10.1007/s12041-020-1182-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Lee K, Kim MS, Lee JS, Bae DN, Jeong N, Yang K, Lee JD, Park JH, Moon JK, Jeong SC. Chromosomal features revealed by comparison of genetic maps of Glycine max and Glycine soja. Genomics 2020; 112:1481-1489. [PMID: 31461668 DOI: 10.1016/j.ygeno.2019.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/08/2019] [Accepted: 08/24/2019] [Indexed: 11/18/2022]
Abstract
Recombination is a crucial component of evolution and breeding. New combinations of variation on chromosomes are shaped by recombination. Recombination is also involved in chromosomal rearrangements. However, recombination rates vary tremendously among chromosome segments. Genome-wide genetic maps are one of the best tools to study variation of recombination. Here, we describe high density genetic maps of Glycine max and Glycine soja constructed from four segregating populations. The maps were used to identify chromosomal rearrangements and find the highly predictable pattern of cross-overs on the broad scale in soybean. Markers on these genetic maps were used to evaluate assembly quality of the current soybean reference genome sequence. We find a strong inversion candidate larger than 3 Mb based on patterns of cross-overs. We also identify quantitative trait loci (QTL) that control number of cross-overs. This study provides fundamental insights relevant to practical strategy for breeding programs and for pan-genome researches.
Collapse
Affiliation(s)
- Kwanghee Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Ju Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Dong Nyuk Bae
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk 55365, Republic of Korea
| | - Kiwoung Yang
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea; Present address, Geolim Pharmaceutical Co., Ltd, QB e centum, 2307, Centumjunggang-ro 90, Heaundae-gu, Busan, Republic of Korea
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Jung-Kyung Moon
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju, Jeonbuk 55365, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea.
| |
Collapse
|
9
|
Oki N, Sayama T, Ishimoto M, Yokota I, Kaga A, Takahashi M, Takahashi M. Quantitative trait loci associated with short inter-node length in soybean. BREEDING SCIENCE 2018; 68:554-560. [PMID: 30697116 PMCID: PMC6345224 DOI: 10.1270/jsbbs.18087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/17/2018] [Indexed: 05/25/2023]
Abstract
Manipulating the genetic control of plant height is essential in soybean breeding to increase yield through the enlargement of the plant size while preventing lodging. A Japanese soybean germplasm, Y2, has distinctively shorter inter-node lengths than those of recently developed Japanese cultivars and is expected to provide new variation to prevent lodging. A quantitative trait loci (QTL) analysis for plant height-related traits was conducted using F2 individuals derived from a cross between the elite Japanese cultivar Fukuyutaka and Y2. A major QTL for average inter-node length (AIL) and plant height was identified on chromosome 13 and named qSI13-1 (QTL for short inter-node on chromosome 13). The Y2 allele of qSI13-1 was partially dominant for plant height. qSI13-1 exhibited no effect on either days to flowering or number of main stem nodes. The AILs and plant heights of the near-isogenic lines containing the Y2 allele of qSI13-1 in the genetic background of Fukuyutaka were significantly less than those of Fukuyutaka. No significant differences between the near-isogenic lines and Fukuyutaka were observed for seed yield and flowering date, indicating that qSI13-1 will be useful in developing cultivars with short plant heights without having negative effects on yield potential and days to flowering.
Collapse
Affiliation(s)
- Nobuhiko Oki
- National Agriculture and Food Research Organization, Kyushu Okinawa Agricultural Research Center,
2421 Suya, Koushi, Kumamoto 861-1192,
Japan
| | - Takashi Sayama
- National Agriculture and Food Research Organization, Western Region Agricultural Research Center,
6-12-1 Nishifukatsu, Fukuyama, Hiroshima 721-8514,
Japan
| | - Masao Ishimoto
- The Institute of Crop Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Ikuko Yokota
- The Institute of Crop Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Akito Kaga
- The Institute of Crop Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Masakazu Takahashi
- National Agriculture and Food Research Organization, Kyushu Okinawa Agricultural Research Center,
2421 Suya, Koushi, Kumamoto 861-1192,
Japan
| | - Motoki Takahashi
- The Institute of Crop Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| |
Collapse
|
10
|
Mishra SS, Behera PK, Kumar V, Lenka SK, Panda D. Physiological characterization and allelic diversity of selected drought tolerant traditional rice ( Oryza sativa L.) landraces of Koraput, India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1035-1046. [PMID: 30425421 PMCID: PMC6214433 DOI: 10.1007/s12298-018-0606-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/17/2018] [Accepted: 09/23/2018] [Indexed: 05/25/2023]
Abstract
Water-deficit stress tolerance in rice is important for maintaining stable yield, especially under rain-fed ecosystem. After a thorough drought-tolerance screening of more than 130 rice genotypes from various regions of Koraput in our previous study, six rice landraces were selected for drought tolerance capacity. These six rice landraces were further used for detailed physiological and molecular assessment under control and simulated drought stress conditions. After imposing various levels of drought stress, leaf photosynthetic rate (PN), photochemical efficiency of photosystem II (Fv/Fm), SPAD chlorophyll index, membrane stability index and relative water content were found comparable with the drought-tolerant check variety (N22). Compared to the drought-susceptible variety IR64, significant positive attributes and varietal differences were observed for all the above physiological parameters in drought-tolerant landraces. Genetic diversity among the studied rice landraces was assessed using 19 previously reported drought tolerance trait linked SSR markers. A total of 50 alleles with an average of 2.6 per locus were detected at the loci of the 19 markers across studied rice genotypes. The Nei's genetic diversity (He) and the polymorphism information content (PIC) ranged from 0.0 to 0.767 and 0.0 to 0.718, respectively. Seven SSR loci, such as RM324, RM19367, RM72, RM246, RM3549, RM566 and RM515, showed the highest PIC values and are thus, useful in assessing the genetic diversity of studied rice lines for drought tolerance. Based on the result, two rice landraces (Pandkagura and Mugudi) showed the highest similarity index with tolerant check variety. However, three rice landraces (Kalajeera, Machhakanta and Haldichudi) are more diverse and showed highest genetic distance with N22. These landraces can be considered as the potential genetic resources for drought breeding program.
Collapse
Affiliation(s)
- Swati S. Mishra
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764 021 India
| | - Prafulla K. Behera
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764 021 India
| | - Vajinder Kumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, 110012 India
| | - Sangram K. Lenka
- TERI, Deakin NanoBiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana 122 001 India
| | - Debabrata Panda
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764 021 India
| |
Collapse
|
11
|
Zhao J, Tang X, Wight CP, Tinker NA, Jiang Y, Yan H, Ma J, Lan X, Wei Y, Ren C, Chen G, Peng Y. Genetic mapping and a new PCR-based marker linked to a dwarfing gene in oat (Avena sativa L.). Genome 2018; 61:497-503. [PMID: 29733232 DOI: 10.1139/gen-2017-0006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloning in the present study were both associated with the dwarfing gene. The two markers were located 21 and 1.2 cM from DwWA, respectively. The bi17 marker was mapped to neighboring SNP markers on chromosome 18D of the oat consensus map. Since Dw6 was previously mapped on chromosome 18, and since our new marker bi17 is also diagnostic for NILs generated for Dw6, there is strong evidence that the dwarfing gene identified in WAOAT2132 is Dw6. The newly developed markers could find applications in the identification of this gene in oat germplasm and in the fine mapping or positional cloning of the gene.
Collapse
Affiliation(s)
- Jun Zhao
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Xueqin Tang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China.,b Agricultural Bureau of Xingwen County, Yibin 644400, Sichuan, China
| | - Charlene P Wight
- c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Nicholas A Tinker
- c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Yunfeng Jiang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Honghai Yan
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China.,c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Jian Ma
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Xiujin Lan
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Yuming Wei
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Changzhong Ren
- d Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Guoyue Chen
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Yuanying Peng
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| |
Collapse
|
12
|
Fujii K, Sayama T, Takagi K, Kosuge K, Okano K, Kaga A, Ishimoto M. Identification and dissection of single seed weight QTLs by analysis of seed yield components in soybean. BREEDING SCIENCE 2018; 68:177-187. [PMID: 29875601 PMCID: PMC5982185 DOI: 10.1270/jsbbs.17098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/23/2017] [Indexed: 05/20/2023]
Abstract
Single seed weight (SSW), or seed size, is a seed yield components (SYC) in soybean, and it is suggested that the genetic factors regulating SSW are involved in the control of other SYCs. The quantitative trait loci (QTLs) for SSW and their effects on the other SYCs were investigated using a recombinant inbred line population derived from typical small- and large-seeded cultivars that were cultivated in two different environments. QTL analysis detected four environmentally stable QTLs for SSW, two of which coincided with the defined loci, qSw17-1 and Ln. The effects of the other loci, qSw12-1 and qSw13-1, were confirmed by analyzing residual heterozygous line progenies derived from the recombinant population. These four QTL regions were also involved in the control of an additional SYC, namely the large-seeded allele at each locus that reduced either the number of pods per plant or the number of ovules per pod. These results suggest the presence of at least two different regulatory mechanisms for SSW. Isolation of genes responsible for these QTLs provides an important tool in the understanding and utilization of SSW diversity for soybean breeding.
Collapse
Affiliation(s)
- Kenichiro Fujii
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Takashi Sayama
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kyoko Takagi
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kazumasa Kosuge
- Plant Biotechnology Institute, Ibaraki Agriculture Center,
3165-1 Ago, Kasama, Ibaraki 319-0206,
Japan
| | - Katsunori Okano
- Plant Biotechnology Institute, Ibaraki Agriculture Center,
3165-1 Ago, Kasama, Ibaraki 319-0206,
Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
| |
Collapse
|
13
|
Ates D, Aldemir S, Alsaleh A, Erdogmus S, Nemli S, Kahriman A, Ozkan H, Vandenberg A, Tanyolac B. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations. PLoS One 2018; 13:e0191375. [PMID: 29351563 PMCID: PMC5774769 DOI: 10.1371/journal.pone.0191375] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022] Open
Abstract
Background Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. Materials and methods A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39). Results The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. Conclusion This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.
Collapse
Affiliation(s)
- Duygu Ates
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Secil Aldemir
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Ahmad Alsaleh
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Semih Erdogmus
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Seda Nemli
- Department of Bieoengineering and Genetics, Gumushane University, Gumushane, Turkey
| | - Abdullah Kahriman
- Department of Field Crops, Faculty of Agriculture, Harran University, Sanlı Urfa, Turkey
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Albert Vandenberg
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Bahattin Tanyolac
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
- * E-mail:
| |
Collapse
|
14
|
Sohn HB, Kim SJ, Hwang TY, Park HM, Lee YY, Markkandan K, Lee D, Lee S, Hong SY, Song YH, Koo BC, Kim YH. Barcode System for Genetic Identification of Soybean [ Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks. FRONTIERS IN PLANT SCIENCE 2017; 8:520. [PMID: 28443113 PMCID: PMC5385371 DOI: 10.3389/fpls.2017.00520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/23/2017] [Indexed: 05/29/2023]
Abstract
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, "Singang" and a recurrent parent, "Sowon" were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.
Collapse
Affiliation(s)
- Hwang-Bae Sohn
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Su-Jeong Kim
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Tae-Young Hwang
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration (RDA)Chungcheongnam-Do, South Korea
| | - Hyang-Mi Park
- Headquarters, National Institute of Crop Science, Rural Development Administration (RDA)Jeolabuk-Do, South Korea
| | - Yu-Young Lee
- Department of Central Area, National Institute of Crop Science, Rural Development Administration (RDA)Gyeonggi-Do, South Korea
| | | | - Dongwoo Lee
- TheragenEtex Bio Institute, TheragenEtex Inc.Gyeonggi-Do, South Korea
| | - Sunghoon Lee
- EONE-DIAGNOMICS Genome CenterIncheon, South Korea
| | - Su-Young Hong
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Yun-Ho Song
- Gangwondo Agricultural Research and Extension ServicesGangwon-Do, South Korea
| | - Bon-Cheol Koo
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Yul-Ho Kim
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| |
Collapse
|
15
|
Li MW, Xin D, Gao Y, Li KP, Fan K, Muñoz NB, Yung WS, Lam HM. Using genomic information to improve soybean adaptability to climate change. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1823-1834. [PMID: 27660480 DOI: 10.1093/jxb/erw348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Climate change has brought severe challenges to agriculture. It is anticipated that there will be a drop in crop yield - including that of soybean - due to climatic stress factors that include drastic fluctuations in temperature, drought, flooding and high salinity. Genomic information on soybean has been accumulating rapidly since initial publication of its reference genome, providing a valuable tool for the improvement of cultivated soybean. Not only are many molecular markers that are associated with important quantitative trait loci now identified, but we also have a more detailed picture of the genomic variations among soybean germplasms, enabling us to utilize these as tools to assist crop breeding. In this review, we will summarize and discuss the currently available soybean genomic approaches, including whole-genome sequencing, sequencing-based genotyping, functional genomics, proteomics, and epigenomics. The information uncovered through these techniques will help further pinpoint important gene candidates and genomic loci associated with adaptive traits, as well as achieving a better understanding of how soybeans cope with the changing climate.
Collapse
Affiliation(s)
- Man-Wah Li
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Dawei Xin
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, College of Science, Northeast Agricultural University, Harbin, Heilongjiang Province, People's Republic of China
| | - Yishu Gao
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kwan-Pok Li
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kejing Fan
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Nacira Belen Muñoz
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias-INTA, Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Wai-Shing Yung
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hon-Ming Lam
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| |
Collapse
|
16
|
Yano R, Takagi K, Takada Y, Mukaiyama K, Tsukamoto C, Sayama T, Kaga A, Anai T, Sawai S, Ohyama K, Saito K, Ishimoto M. Metabolic switching of astringent and beneficial triterpenoid saponins in soybean is achieved by a loss-of-function mutation in cytochrome P450 72A69. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:527-539. [PMID: 27775214 DOI: 10.1111/tpj.13403] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 05/24/2023]
Abstract
Triterpenoid saponins are major components of secondary metabolites in soybean seeds and are divided into two groups: group A saponins, and 2,3-dihydro-2,5-dihydroxy-6-methyl-4H-pyran-4-one (DDMP) saponins. The aglycone moiety of group A saponins consists of soyasapogenol A (SA), which is an oxidized β-amyrin product, and the aglycone moiety of the DDMP saponins consists of soyasapogenol B (SB). Group A saponins produce a bitter and astringent aftertaste in soy products, whereas DDMP saponins have known health benefits for humans. We completed map-based cloning and characterization of the gene Sg-5, which is responsible for SA biosynthesis. The naturally occurring sg-5 mutant lacks group A saponins and has a loss-of-function mutation (L164*) in Glyma15g39090, which encodes the cytochrome P450 enzyme, CYP72A69. An enzyme assay indicated the hydroxylase activity of recombinant CYP72A69 against SB, which also suggested the production of SA. Additionally, induced Glyma15g39090 mutants (R44* or S348P) lacked group A saponins similar to the sg-5 mutant, indicating that Glyma15g39090 corresponds to Sg-5. Endogenous levels of DDMP saponins were higher in the sg-5 mutant than in the wild-type lines due to the loss of the enzyme activity that converts SB to SA. Interestingly, the genomes of palaeopolyploid soybean and the closely related common bean carry multiple Sg-5 paralogs in a genomic region syntenic to the soybean Sg-5 region. However, SA did not accumulate in common bean samples, suggesting that Sg-5 activity evolved after gene duplication event(s). Our results demonstrate that metabolic switching of undesirable saponins with beneficial saponins can be achieved in soybean by disabling Sg-5.
Collapse
Affiliation(s)
- Ryoichi Yano
- National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kyoko Takagi
- National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yoshitake Takada
- Western Region Agricultural Research Center, NARO, 1-3-1 Senyu, Zentsuji, Kagawa, 765-8508, Japan
| | - Kyosuke Mukaiyama
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Chigen Tsukamoto
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Takashi Sayama
- National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Akito Kaga
- National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Genetic Resources Center, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Toyoaki Anai
- Laboratory of Plant Genetics and Breeding, Faculty of Agriculture, Saga University, Honjyo-machi 1, Saga, 840-8502, Japan
| | - Satoru Sawai
- RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kiyoshi Ohyama
- RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, Oh-okayama 2-12-1, Meguro-ku, Tokyo, 152-8551, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675, Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| |
Collapse
|
17
|
Watanabe D, Adányi N, Takács K, Maczó A, Nagy A, Gelencsér É, Pachner M, Lauter K, Baumgartner S, Vollmann J. Development of soybeans with low P34 allergen protein concentration for reduced allergenicity of soy foods. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:1010-1017. [PMID: 27247268 DOI: 10.1002/jsfa.7827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 01/04/2016] [Accepted: 05/25/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND In soybean, at least 16 seed proteins have been identified as causing allergenic reactions in sensitive individuals. As a soybean genebank accession low in the immunodominant protein P34 (Gly m Bd 30K) has recently been found, introgression of the low-P34 trait into adapted soybean germplasm has been attempted in order to improve the safety of food products containing soybean protein. Therefore, marker-assisted selection and proteomics were applied to identify and characterize low-P34 soybeans. RESULTS In low-P34 lines selected from a cross-population, concentrations of the P34 protein as identified with a polyclonal antibody were reduced by 50-70% as compared to P34-containing controls. Using 2D electrophoresis and immunoblotting, the reduction of P34 protein was verified in low-P34 lines. This result was confirmed by liquid chromatographic-tandem mass spectrometric analysis, which revealed either a reduction or complete absence of the authentic P34 protein as suggested from presence or absence of a unique peptide useful for discriminating between conventional and low-P34 lines. CONCLUSION Marker-assisted selection proved useful for identifying low-P34 soybean lines for the development of hypoallergenic soy foods. The status of the P34 protein in low-P34 lines needs further characterization. In addition, the food safety relevance of low-P34 soybeans should be tested in clinical studies. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Daisuke Watanabe
- Department of Crop Sciences, Division of Plant Breeding, University of Natural Resources and Life Sciences Vienna (BOKU), 3430, Tulln an der Donau, Austria
| | - Nóra Adányi
- National Agricultural Research and Innovation Centre, Food Science Research Institute (NARIC-FSRI), 1022, Budapest, Hungary
| | - Krisztina Takács
- National Agricultural Research and Innovation Centre, Food Science Research Institute (NARIC-FSRI), 1022, Budapest, Hungary
| | - Anita Maczó
- National Agricultural Research and Innovation Centre, Food Science Research Institute (NARIC-FSRI), 1022, Budapest, Hungary
| | - András Nagy
- National Agricultural Research and Innovation Centre, Food Science Research Institute (NARIC-FSRI), 1022, Budapest, Hungary
| | - Éva Gelencsér
- National Agricultural Research and Innovation Centre, Food Science Research Institute (NARIC-FSRI), 1022, Budapest, Hungary
| | - Martin Pachner
- Department of Crop Sciences, Division of Plant Breeding, University of Natural Resources and Life Sciences Vienna (BOKU), 3430, Tulln an der Donau, Austria
| | - Kathrin Lauter
- Department IFA-Tulln, Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 3430, Tulln an der Donau, Austria
| | - Sabine Baumgartner
- Department IFA-Tulln, Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 3430, Tulln an der Donau, Austria
| | - Johann Vollmann
- Department of Crop Sciences, Division of Plant Breeding, University of Natural Resources and Life Sciences Vienna (BOKU), 3430, Tulln an der Donau, Austria
| |
Collapse
|
18
|
|
19
|
Kan G, Ning L, Li Y, Hu Z, Zhang W, He X, Yu D. Identification of novel loci for salt stress at the seed germination stage in soybean. BREEDING SCIENCE 2016; 66:530-541. [PMID: 27795678 PMCID: PMC5010299 DOI: 10.1270/jsbbs.15147] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/02/2016] [Indexed: 05/09/2023]
Abstract
Salt tolerance in soybean [Glycine max (L.) Merr.] at the seed germination stage is a critical determinant of stable stand establishment in saline soil. This study examined one population of 184 recombinant inbred lines (RILs, F7:11) derived from a cross between Kefeng1 and Nannong1138-2 and one natural population consisting of 196 soybean landraces. A total of 11 quantitative trait loci (QTLs) and 22 simple sequence repeat (SSR) loci associated with three salt tolerance indices were detected by linkage and association mapping. The SSR marker Sat_162 was found to be closely linked to the co-localized QTLs at a site 792,811 bp from the gene Glyma08g12400.1, which was verified in response to salt stress at the germination stage. Five SSR markers, Satt201, BE475343, CSSR306, Satt664 and Satt567, were co-associated with two of the salt tolerance indices, and two SSR markers, Satt156 and Satt636, were co-associated with all three salt tolerance indices. Furthermore, elite alleles and their carrier materials were identified by analyzing alleles at the loci associated with these salt tolerance indices. These results may be beneficial for the future breeding of soybean salt tolerance at the germination stage using marker-assisted selection and molecular pyramiding breeding.
Collapse
Affiliation(s)
- Guizhen Kan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Lihua Ning
- Provincial Key Laboratory of Agrobiology, Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences,
Nanjing 210014,
China
| | - Yakai Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Zhenbin Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Xiaohong He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
- Corresponding author (e-mail: )
| |
Collapse
|
20
|
Takeshima R, Hayashi T, Zhu J, Zhao C, Xu M, Yamaguchi N, Sayama T, Ishimoto M, Kong L, Shi X, Liu B, Tian Z, Yamada T, Kong F, Abe J. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5247-58. [PMID: 27422993 PMCID: PMC5014162 DOI: 10.1093/jxb/erw283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
FLOWERING LOCUS T (FT) is an important floral integrator whose functions are conserved across plant species. In soybean, two orthologs, FT2a and FT5a, play a major role in initiating flowering. Their expression in response to different photoperiods is controlled by allelic combinations at the maturity loci E1 to E4, generating variation in flowering time among cultivars. We determined the molecular basis of a quantitative trait locus (QTL) for flowering time in linkage group J (Chromosome 16). Fine-mapping delimited the QTL to a genomic region of 107kb that harbors FT5a We detected 15 DNA polymorphisms between parents with the early-flowering (ef) and late-flowering (lf) alleles in the promoter region, an intron, and the 3' untranslated region of FT5a, although the FT5a coding regions were identical. Transcript abundance of FT5a was higher in near-isogenic lines for ef than in those for lf, suggesting that different transcriptional activities or mRNA stability caused the flowering time difference. Single-nucleotide polymorphism (SNP) calling from re-sequencing data for 439 cultivated and wild soybean accessions indicated that ef is a rare haplotype that is distinct from common haplotypes including lf The ef allele at FT5a may play an adaptive role at latitudes where early flowering is desirable.
Collapse
Affiliation(s)
- Ryoma Takeshima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Takafumi Hayashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Jianghui Zhu
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Chen Zhao
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Meilan Xu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Memuro, Hokkaido 082-0081, Japan
| | - Takashi Sayama
- National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences, Kannondai, Ibaraki 305-8602, Japan
| | - Lingping Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xinyi Shi
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 1001014, China
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| |
Collapse
|
21
|
Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Deutsch J, Salazar W, Hernandez-Ochoa M, Grygleski E, Steffan S, Iorizzo M, Polashock J, Vorsa N, Zalapa J. Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping. BMC Genomics 2016; 17:451. [PMID: 27295982 PMCID: PMC4906896 DOI: 10.1186/s12864-016-2802-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 05/27/2016] [Indexed: 01/08/2023] Open
Abstract
Background The application of genotyping by sequencing (GBS) approaches, combined with data imputation methodologies, is narrowing the genetic knowledge gap between major and understudied, minor crops. GBS is an excellent tool to characterize the genomic structure of recently domesticated (~200 years) and understudied species, such as cranberry (Vaccinium macrocarpon Ait.), by generating large numbers of markers for genomic studies such as genetic mapping. Results We identified 10842 potentially mappable single nucleotide polymorphisms (SNPs) in a cranberry pseudo-testcross population wherein 5477 SNPs and 211 short sequence repeats (SSRs) were used to construct a high density linkage map in cranberry of which a total of 4849 markers were mapped. Recombination frequency, linkage disequilibrium (LD), and segregation distortion at the genomic level in the parental and integrated linkage maps were characterized for first time in cranberry. SSR markers, used as the backbone in the map, revealed high collinearity with previously published linkage maps. The 4849 point map consisted of twelve linkage groups spanning 1112 cM, which anchored 2381 nuclear scaffolds accounting for ~13 Mb of the estimated 470 Mb cranberry genome. Bin mapping identified 592 and 672 unique bins in the parentals and a total of 1676 unique marker positions in the integrated map. Synteny analyses comparing the order of anchored cranberry scaffolds to their homologous positions in kiwifruit, grape, and coffee genomes provided initial evidence of homology between cranberry and closely related species. Conclusions GBS data was used to rapidly saturate the cranberry genome with markers in a pseudo-testcross population. Collinearity between the present saturated genetic map and previous cranberry SSR maps suggests that the SNP locations represent accurate marker order and chromosome structure of the cranberry genome. SNPs greatly improved current marker genome coverage, which allowed for genome-wide structure investigations such as segregation distortion, recombination, linkage disequilibrium, and synteny analyses. In the future, GBS can be used to accelerate cranberry molecular breeding through QTL mapping and genome-wide association studies (GWAS). Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2802-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Luis Diaz-Garcia
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA.,Instituto Nacional de Investigaciones Agrícolas, Forestales y Pecuarias, Campo Experimental Pabellón, Aguascalientes, Mexico
| | - Brandon Schlautman
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA
| | - Joseph Deutsch
- Department of Statistics, University of Wisconsin, Madison, Wisconsin, USA
| | - Walter Salazar
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA
| | | | | | - Shawn Steffan
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, USA
| | - Massimo Iorizzo
- Department of Horticultural Sciences, Plants for Human Health Institute, North Carolina State University, Kannapolis, North Carolina, USA
| | - James Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, New Jersey, USA
| | - Nicholi Vorsa
- Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, New Jersey, USA
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA. .,USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, Wisconsin, USA.
| |
Collapse
|
22
|
Preliminary genetic linkage map of Indian major carp, Labeo rohita (Hamilton 1822) based on microsatellite markers. J Genet 2016; 94:271-7. [PMID: 26174674 DOI: 10.1007/s12041-015-0528-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Linkage map with wide marker coverage is an essential resource for genetic improvement study for any species. Sex-averaged genetic linkage map of Labeo rohita, popularly known as 'rohu', widely cultured in the Indian subcontinent, was developed by placing 68 microsatellite markers generated by a simplified method. The parents and their F1 progeny (92 individuals) were used as segregating populations. The genetic linkage map spans a sex-averaged total length of 1462.2 cM, in 25 linkage groups. The genome length of rohu was estimated to be 3087.9 cM. This genetic linkage map may facilitate systematic searches of the genome to identify genes associated with commercially important characters and marker-assisted selection programmes of this species.
Collapse
|
23
|
Song X, Wei H, Cheng W, Yang S, Zhao Y, Li X, Luo D, Zhang H, Feng X. Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean. G3 (BETHESDA, MD.) 2015; 5:2793-9. [PMID: 26483012 PMCID: PMC4683650 DOI: 10.1534/g3.115.022780] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/10/2015] [Indexed: 02/04/2023]
Abstract
Soybean [Glycine max (L.) Merrill] is an important crop worldwide. In this study, a Chinese local soybean cultivar, Hedou 12, was resequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for genetic mapping. 49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5-50 bp in length were chosen for validation, and 165 (68%) of them revealed polymorphisms between Hedou 12 and Williams 82. The validated INDEL markers were also tested in 12 other soybean cultivars. The number of polymorphisms in the pairwise comparisons of 14 soybean cultivars varied from 27 to 165. To test the utility of these INDEL markers, they were used to perform genetic mapping of a crinkly leaf mutant, and the CRINKLY LEAF locus was successfully mapped to a 360 kb region on chromosome 7. This research shows that high-throughput sequencing technologies can facilitate the development of genome-wide molecular markers for genetic mapping in soybean.
Collapse
Affiliation(s)
- Xiaofeng Song
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China
| | - Haichao Wei
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 130102 Changchun, China
| | - Wen Cheng
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 130102 Changchun, China
| | - Yanxiu Zhao
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, China
| | - Da Luo
- School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China
| | - Hui Zhang
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China
| | - Xianzhong Feng
- Key Laboratory of Systems Biology in Universities of Shandong, College of Life Science, Shandong Normal University, 250014 Jinan, China Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 130102 Changchun, China
| |
Collapse
|
24
|
Yang T, Fang L, Zhang X, Hu J, Bao S, Hao J, Li L, He Y, Jiang J, Wang F, Tian S, Zong X. High-Throughput Development of SSR Markers from Pea (Pisum sativum L.) Based on Next Generation Sequencing of a Purified Chinese Commercial Variety. PLoS One 2015; 10:e0139775. [PMID: 26440522 PMCID: PMC4595016 DOI: 10.1371/journal.pone.0139775] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/17/2015] [Indexed: 11/18/2022] Open
Abstract
Pea (Pisum sativum L.) is an important food legume globally, and is the plant species that J.G. Mendel used to lay the foundation of modern genetics. However, genomics resources of pea are limited comparing to other crop species. Application of marker assisted selection (MAS) in pea breeding has lagged behind many other crops. Development of a large number of novel and reliable SSR (simple sequence repeat) or microsatellite markers will help both basic and applied genomics research of this crop. The Illumina HiSeq 2500 System was used to uncover 8,899 putative SSR containing sequences, and 3,275 non-redundant primers were designed to amplify these SSRs. Among the 1,644 SSRs that were randomly selected for primer validation, 841 yielded reliable amplifications of detectable polymorphisms among 24 genotypes of cultivated pea (Pisum sativum L.) and wild relatives (P. fulvum Sm.) originated from diverse geographical locations. The dataset indicated that the allele number per locus ranged from 2 to 10, and that the polymorphism information content (PIC) ranged from 0.08 to 0.82 with an average of 0.38. These 1,644 novel SSR markers were also tested for polymorphism between genotypes G0003973 and G0005527. Finally, 33 polymorphic SSR markers were anchored on the genetic linkage map of G0003973 × G0005527 F2 population.
Collapse
Affiliation(s)
- Tao Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Fang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyan Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Jinguo Hu
- USDA-ARS Western Regional Plant Introduction Station, Pullman, Washington, United States of America
| | - Shiying Bao
- Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Junjie Hao
- Qingdao Academy of Agricultural Sciences, Qingdao, China
| | - Ling Li
- Institute of Cash Crops, Liaoning Academy of Agricultural Sciences, Liaoyang, China
| | - Yuhua He
- Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Junye Jiang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fang Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shufang Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuxiao Zong
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
25
|
Verma P, Goyal R, Chahota RK, Sharma TR, Abdin MZ, Bhatia S. Construction of a Genetic Linkage Map and Identification of QTLs for Seed Weight and Seed Size Traits in Lentil (Lens culinaris Medik.). PLoS One 2015; 10:e0139666. [PMID: 26436554 PMCID: PMC4593543 DOI: 10.1371/journal.pone.0139666] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 09/16/2015] [Indexed: 01/05/2023] Open
Abstract
Seed weight and seed size both are quantitative traits and have been considered as important components of grain yield, thus identification of quantitative trait loci (QTL) for seed traits in lentil (Lens culinaris) would be beneficial for the improvement of grain yield. Hence the main objective of this study was to identify QTLs for seed traits using an intraspecific mapping population derived from a cross between L. culinaris cv. Precoz (seed weight-5.1g, seed size-5.7mm) and L. culinaris cv. L830 (seed weight-2.2g, seed size-4mm) comprising 126 F8-RILs. For this, two microsatellite genomic libraries enriched for (GA/CT) and (GAA/CTT) motif were constructed which resulted in the development of 501 new genomic SSR markers. Six hundred forty seven SSR markers (including 146 previously published) were screened for parental polymorphism and 219 (33.8%) were found to be polymorphic among the parents. Of these 216 were mapped on seven linkage groups at LOD4.0 spanning 1183.7cM with an average marker density of 5.48cM. Phenotypic data from the RILs was used to identify QTLs for the seed weight and seed size traits by single marker analysis (SMA) followed by composite interval mapping (CIM) which resulted in one QTL each for the 2 traits (qSW and qSS) that were co-localized on LG4 and explained 48.4% and 27.5% of phenotypic variance respectively. The current study would serve as a strong foundation for further validation and fine mapping for utilization in lentil breeding programs.
Collapse
Affiliation(s)
- Priyanka Verma
- National Institute of Plant Genome Research, Post Box No. 10531, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, 110062, India
| | - Richa Goyal
- National Institute of Plant Genome Research, Post Box No. 10531, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - R. K. Chahota
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, 176 062, India
| | - Tilak R. Sharma
- Department of Agricultural Biotechnology, Chaudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, 176 062, India
| | - M. Z. Abdin
- Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, 110062, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Post Box No. 10531, Aruna Asaf Ali Marg, New Delhi, 110067, India
| |
Collapse
|
26
|
Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2015; 6:367. [PMID: 26074933 PMCID: PMC4444744 DOI: 10.3389/fpls.2015.00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/09/2015] [Indexed: 05/18/2023]
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
Collapse
Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Kanikar Theerawattanasuk
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kanlaya Nirapathpongporn
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Phayao Romruensukharom
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
- *Correspondence: Sithichoke Tangphatsornruang, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
27
|
Yamaguchi N, Sayama T, Yamazaki H, Miyoshi T, Ishimoto M, Funatsuki H. Quantitative trait loci associated with lodging tolerance in soybean cultivar 'Toyoharuka'. BREEDING SCIENCE 2014; 64:300-8. [PMID: 25914584 PMCID: PMC4267304 DOI: 10.1270/jsbbs.64.300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/20/2014] [Indexed: 05/10/2023]
Abstract
Lodging tolerance (LT) is an important trait for high yield and combine-harvesting efficiency in soybean [Glycine max (L.) Merr.]. Many previous studies have investigated quantitative trait loci (QTLs) for lodging score (LS) in soybean. Most of the investigated QTLs were located in the proximal region of maturity or growth habit loci. The aim of this study was to identify genetic factors for LT not associated with maturity or growth habit. QTL analysis was performed using a recombinant inbred line (RIL) population derived from a cross between 'Toyoharuka' (TH), a lodging-tolerant cultivar, and 'Toyomusume' (TM). The genotypes of TH and TM were estimated as both e1e2E3E4 and dt1. The average LS over 4 years was used for QTL analysis, identifying a major and stable QTL, qLS19-1, on chromosome 19. The LS of the near-isogenic line (NIL) with the TH allele at Sat_099, the nearest marker to qLS19-1, was significantly lower than the NIL with the TM allele at that position. The TH allele at Sat_099 rarely had a negative influence on seed yield or other agronomic traits in both NILs and the TM-backcrossed lines. Our results suggest that marker-assisted selection for qLS19-1 is effective for improving LT in breeding programs.
Collapse
Affiliation(s)
- Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station,
2, Minami 9 sen, Shinsei, Memuro, Kasai, Hokkaido 082-0081,
Japan
- Corresponding author (e-mail: )
| | - Takashi Sayama
- National Institute of Agrobiological Sciences,
2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hiroyuki Yamazaki
- Hokkaido Research Organization Tokachi Agricultural Experiment Station,
2, Minami 9 sen, Shinsei, Memuro, Kasai, Hokkaido 082-0081,
Japan
- Present address: Hokkaido Research Organization Agricultural Research Department, Higashi 6 sen Kita 15 Gou, Naganuma, Yubari, Hokkaido 069-1395, Japan
| | - Tomoaki Miyoshi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station,
2, Minami 9 sen, Shinsei, Memuro, Kasai, Hokkaido 082-0081,
Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences,
2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hideyuki Funatsuki
- NARO Western Region Agricultural Research Center,
6-12-1 Nishifukatsu, Fukuyama, Hiroshima 721-8514,
Japan
| |
Collapse
|
28
|
Yamada T, Shimada S, Hajika M, Hirata K, Takahashi K, Nagaya T, Hamaguchi H, Maekawa T, Sayama T, Hayashi T, Ishimoto M, Tanaka J. Major QTLs associated with green stem disorder insensitivity of soybean (Glycine max (L.) Merr.). BREEDING SCIENCE 2014; 64:331-338. [PMID: 25914587 PMCID: PMC4267307 DOI: 10.1270/jsbbs.64.331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 08/29/2014] [Indexed: 06/04/2023]
Abstract
Green stem disorder (GSD) is one of the most serious syndromes affecting soybean (Glycine max) cultivation in Japan. In GSD, stems remain green even when pods mature. When soybean plants develop GSD, seed surfaces are soiled by tissue fluid and seed quality is deteriorated during machine harvesting. We performed quantitative trait locus (QTL) analyses for GSD insensitivity using recombinant inbred lines (RILs; n = 154) derived from a cross between an insensitive line ('Touhoku 129') and a sensitive leading cultivar ('Tachinagaha') during a 6-year evaluation. Three effective QTLs were detected. The influences of these QTLs were in the following order: qGSD1 (LG_H) > qGSD2 (LG_F) > qGSD3 (LG_L). At these three QTLs, 'Touhoku 129' genotypes exhibited more GSD insensitivity than 'Tachinagaha' genotypes. The lower incidence of GSD for 'Touhoku129' was attributable primarily to these three QTLs because RILs harboring a 'Touhoku 129' genotype at the three QTLs exhibited a GSD incidence similar to that of 'Touhoku 129.' Although a limitation of this study is that only one mapping population was evaluated, this QTL information and the flanking markers of these QTLs would be effective tools for resolving GSD in soybean breeding programs.
Collapse
Affiliation(s)
- Tetsuya Yamada
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Shinji Shimada
- NARO Agricultural Research Center (NARO/ARC),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517,
Japan
| | - Makita Hajika
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Kaori Hirata
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- NARO Tohoku Agricultural Research Center (NARO/TARC),
297 Uenodai, Kariwano, Daisen, Akita 019-2112,
Japan
| | - Koji Takahashi
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Taiko Nagaya
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Hideo Hamaguchi
- NARO Agricultural Research Center (NARO/ARC),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517,
Japan
| | - Tomiya Maekawa
- NARO Agricultural Research Center (NARO/ARC),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517,
Japan
| | - Takashi Sayama
- National Institute of Agrobiological Science (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Takeshi Hayashi
- NARO Agricultural Research Center (NARO/ARC),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517,
Japan
- Graduate School of Life and Environmental Science, University of Tsukuba,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Science (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Junichi Tanaka
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Graduate School of Life and Environmental Science, University of Tsukuba,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| |
Collapse
|
29
|
Hirata K, Masuda R, Tsubokura Y, Yasui T, Yamada T, Takahashi K, Nagaya T, Sayama T, Ishimoto M, Hajika M. Identification of quantitative trait loci associated with boiled seed hardness in soybean. BREEDING SCIENCE 2014; 64:362-70. [PMID: 25914591 PMCID: PMC4267311 DOI: 10.1270/jsbbs.64.362] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 09/21/2014] [Indexed: 05/06/2023]
Abstract
Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, 'Natto-shoryu' and 'Hyoukei-kuro 3', which differ largely in boiled seed hardness, which in 'Natto-shoryu' is about twice that of 'Hyoukei-kuro 3'. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the 'Hyoukei-kuro 3' alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.
Collapse
Affiliation(s)
- Kaori Hirata
- NARO Tohoku Agricultural Research Center,
297 Uenodai, Kariwano, Daisen, Akita 019-2112,
Japan
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
- Corresponding author (e-mail: )
| | - Ryoichi Masuda
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Yasutaka Tsubokura
- Snow Brand Seed Company, Limited,
634 Naganumahara, Inage, Chiba 263-0001,
Japan
| | - Takeshi Yasui
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Tetsuya Yamada
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Koji Takahashi
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Taiko Nagaya
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Takashi Sayama
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Makita Hajika
- NARO Institute of Crop Science (NICS),
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| |
Collapse
|
30
|
Morisaki A, Yamada N, Yamanaka S, Matsui K. Dimethyl sulfide as a source of the seaweed-like aroma in cooked soybeans and correlation with its precursor, S-methylmethionine (vitamin U). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:8289-94. [PMID: 25090616 DOI: 10.1021/jf501614j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Among the soybean germplasm in Japan, two varieties, Nishiyamahitashi 98-5 (NH) and Shinanokurakake (SKK), have an intense seaweed-like flavor after cooking. Gas-liquid chromatography with mass spectrometry (GC-MS) indicated that a significant amount (11.5 ± 3.46 μg g(-1) for NH and 6.66 ± 0.91 μg g(-1) for SKK) of dimethyl sulfide (DMS) was formed after heat treatment. DMS is formed from S-methylmethionine (SMM, vitamin U). SMM was detected in all soybean varieties examined here, but its concentration in NH and SKK seeds was >100-fold higher than in the other varieties and ranged from 75 to 290 μg g(-1). The SMM content and the ability to form DMS upon heat treatment correlated among them. The plumes and radicles contained SMM exclusively. This is the first report of soybean varieties containing SMM at a level equivalent to or higher than that in vegetables known to contain high levels of SMM, for example, turnip, cabbage, and celery.
Collapse
Affiliation(s)
- Akira Morisaki
- Graduate School of Medicine (Agriculture) and Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University , Yamaguchi 753-8515, Japan
| | | | | | | |
Collapse
|
31
|
Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song Q, Schultz Q, Qi L. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One 2014; 9:e98628. [PMID: 25014030 PMCID: PMC4094432 DOI: 10.1371/journal.pone.0098628] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/06/2014] [Indexed: 11/19/2022] Open
Abstract
A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.
Collapse
Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Li Gong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Brent S. Hulke
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
| | | | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA- Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Quentin Schultz
- BioDiagnostics Inc., River Falls, Wisconsin, United States of America
| | - Lili Qi
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
- * E-mail:
| |
Collapse
|
32
|
Kato S, Sayama T, Fujii K, Yumoto S, Kono Y, Hwang TY, Kikuchi A, Takada Y, Tanaka Y, Shiraiwa T, Ishimoto M. A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1365-74. [PMID: 24718925 DOI: 10.1007/s00122-014-2304-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/24/2014] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE We detected a QTL for single seed weight in soybean that was stable across multiple environments and genetic backgrounds with the use of two recombinant inbred line populations. Single seed weight (SSW) in soybean is a key determinant of both seed yield and the quality of soy food products, and it exhibits wide variation. SSW is under genetic control, but the molecular mechanisms of such control remain unclear. We have now investigated quantitative trait loci (QTLs) for SSW in soybean and have identified such a QTL that is stable across multiple environments and genetic backgrounds. Two populations of 225 and 250 recombinant inbred lines were developed from crosses between Japanese and US cultivars of soybean that differ in SSW by a factor of ~2, and these populations were grown in at least three different environments. A whole-genome panel comprising 304 simple sequence repeat (SSR) loci was applied to mapping in each population. We identified 15 significant QTLs for SSW dispersed among 11 chromosomes in the two populations. One QTL located between Sat_284 and Sat_292 on chromosome 17 was detected (3.6 < LOD < 14.1) in both populations grown in all environments. This QTL, tentatively designated qSw17-1, accounted for 9.4-20.9 % of phenotypic variation in SSW, with a dominant allele being associated with increased SSW. Given its substantial effect on SSW, qSw17-1 is an attractive target for positional cloning, and SSR markers closely associated with this locus may prove useful for marker-assisted selection for SSW control in soybean.
Collapse
Affiliation(s)
- Shin Kato
- National Agriculture and Food Research Organization (NARO) Tohoku Region Agricultural Research Center, 297 Uenodai, Kariwano, Daisen, Akita, 019-2112, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Li YH, Liu YL, Reif JC, Liu ZX, Liu B, Mette MF, Chang RZ, Qiu LJ. Biparental resequencing coupled with SNP genotyping of a segregating population offers insights into the landscape of recombination and fixed genomic regions in elite soybean. G3 (BETHESDA, MD.) 2014; 4:553-60. [PMID: 24476671 PMCID: PMC4059229 DOI: 10.1534/g3.113.009589] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 01/24/2014] [Indexed: 11/18/2022]
Abstract
Identification of genes underlying agronomic traits is dependent on the segregation of quantitative trait loci (QTL). A popular hypothesis is that elite lines are becoming increasingly similar to each other, resulting in large genomic regions with fixed genes. Here, we resequenced two parental modern elite soybean lines [ZhongHuang13 (ZH) and ZhongPin03-5373 (ZP)] and discovered 794,876 SNPs with reference to the published Williams82 genome. SNPs were distributed unevenly across the chromosomes, with 87.1% of SNPs clustering in 4.9% of the soybean reference genome. Most of the regions with a high density of SNP polymorphisms were located in the chromosome arms. Moreover, seven large regions that were highly similar between parental lines were identified. A GoldenGate SNP genotyping array was designed using 384 SNPs and the 254 recombinant inbred lines (F8) derived from the cross of ZP × ZH were genotyped. We constructed a genetic linkage map using a total of 485 molecular markers, including 313 SNPs from the array, 167 simple sequence repeats (SSRs), 4 expressed sequence tag-derived SSRs, and 1 insertion/deletion marker. The total length of the genetic map was 2594.34 cM, with an average marker spacing of 5.58 cM. Comparing physical and genetic distances, we found 20 hotspot and 14 coldspot regions of recombination. Our results suggest that the technology of resequencing of parental lines coupled with high-throughput SNP genotyping could efficiently bridge the genotyping gap and provide deep insights into the landscape of recombination and fixed genomic regions in biparental segregating populations of soybean with implications for fine mapping of QTL.
Collapse
Affiliation(s)
- Ying-hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Yu-lin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Jochen C. Reif
- Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Stadt Seeland, Gatersleben, Germany
| | - Zhang-xiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Bo Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Michael F. Mette
- Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Stadt Seeland, Gatersleben, Germany
| | - Ru-zhen Chang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Li-juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| |
Collapse
|
34
|
Hu Z, Zhang D, Zhang G, Kan G, Hong D, Yu D. Association mapping of yield-related traits and SSR markers in wild soybean (Glycine soja Sieb. and Zucc.). BREEDING SCIENCE 2014; 63:441-9. [PMID: 24757383 PMCID: PMC3949580 DOI: 10.1270/jsbbs.63.441] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 11/11/2013] [Indexed: 05/21/2023]
Abstract
Wild soybean, the progenitor of cultivated soybean, is an important gene pool for ongoing soybean breeding efforts. To identify yield-enhancing quantitative trait locus (QTL) or gene from wild soybean, 113 wild soybeans accessions were phenotyped for five yield-related traits and genotyped with 85 simple sequence repeat (SSR) markers to conduct association mapping. A total of 892 alleles were detected for the 85 SSR markers, with an average 10.49 alleles; the corresponding PIC values ranged from 0.07 to 0.92, with an average 0.73. The genetic diversity of each SSR marker ranged from 0.07 to 0.93, with an average 0.75. A total of 18 SSR markers were identified for the five traits. Two SSR markers, sct_010 and satt316, which are associated with the yield per plant were stably expressed over two years at two experimental locations. Our results suggested that association mapping can be an effective approach for identifying QTL from wild soybean.
Collapse
Affiliation(s)
- Zhenbin Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
- Henan Center of Crop Design, Henan Academy of Agricultural Science,
Zhengzhou 450002,
China
| | - Dan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
- Department of Agronomy, Henan Agricultural University,
Zhengzhou 450002,
China
| | - Guozheng Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Guizhen Kan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Delin Hong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University,
Nanjing 210095,
China
- Corresponding author (e-mail: )
| |
Collapse
|
35
|
Satovic Z, Avila CM, Cruz-Izquierdo S, Díaz-Ruíz R, García-Ruíz GM, Palomino C, Gutiérrez N, Vitale S, Ocaña-Moral S, Gutiérrez MV, Cubero JI, Torres AM. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.). BMC Genomics 2013; 14:932. [PMID: 24377374 PMCID: PMC3880837 DOI: 10.1186/1471-2164-14-932] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/12/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. RESULTS A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. CONCLUSION We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications.
Collapse
Affiliation(s)
- Zlatko Satovic
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Present addresses: Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Carmen M Avila
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Serafin Cruz-Izquierdo
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Recursos Genéticos y Productividad – Genética, Campus Montecillo, Km 36.5 Carretera México-Texcoco, C.P., Texcoco, Edo. de México 56230, México
| | - Ramón Díaz-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
- Colegio de Postgraduados, Campus Puebla, Km 125.5 Carretera México-Puebla, C.P., Puebla, Pue 72760, México
| | - Gloria M García-Ruíz
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Carmen Palomino
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Natalia Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Stefania Vitale
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - Sara Ocaña-Moral
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - María Victoria Gutiérrez
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| | - José I Cubero
- Departamento de Mejora Genética, IAS-CSIC, Apdo. 4084, Córdoba 14080, Spain
| | - Ana M Torres
- IFAPA, Centro Alameda del Obispo, Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, Córdoba 14080, Spain
| |
Collapse
|
36
|
Andriantahina F, Liu X, Huang H. Genetic map construction and quantitative trait locus (QTL) detection of growth-related traits in Litopenaeus vannamei for selective breeding applications. PLoS One 2013; 8:e75206. [PMID: 24086466 PMCID: PMC3783498 DOI: 10.1371/journal.pone.0075206] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/10/2013] [Indexed: 11/19/2022] Open
Abstract
Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL) have been regarded as useful for marker-assisted selection (MAS) in complex traits as growth. Using an intermediate F2 cross of slow and fast growth parents, a genetic linkage map of Pacific whiteleg shrimp, Litopenaeusvannamei, based on amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers was constructed. Meanwhile, QTL analysis was performed for growth-related traits. The linkage map consisted of 451 marker loci (429 AFLPs and 22 SSRs) which formed 49 linkage groups with an average marker space of 7.6 cM; they spanned a total length of 3627.6 cM, covering 79.50% of estimated genome size. 14 QTLs were identified for growth-related traits, including three QTLs for body weight (BW), total length (TL) and partial carapace length (PCL), two QTLs for body length (BL), one QTL for first abdominal segment depth (FASD), third abdominal segment depth (TASD) and first abdominal segment width (FASW), which explained 2.62 to 61.42% of phenotypic variation. Moreover, comparison of linkage maps between L. vannamei and Penaeusjaponicus was applied, providing a new insight into the genetic base of QTL affecting the growth-related traits. The new results will be useful for conducting MAS breeding schemes in L. vannamei .
Collapse
Affiliation(s)
- Farafidy Andriantahina
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People’s Republic of China
| | - Xiaolin Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, People’s Republic of China
| | - Hao Huang
- Hainan Guangtai Ocean Breeding Company Limited, Haikou, People’s Republic of China
| |
Collapse
|
37
|
Lee WK, Kim N, Kim J, Moon JK, Jeong N, Choi IY, Kim SC, Chung WH, Kim HS, Lee SH, Jeong SC. Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1103-19. [PMID: 23306355 DOI: 10.1007/s00122-012-2039-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 12/21/2012] [Indexed: 05/02/2023]
Abstract
Despite the intensive soybean [Glycine max (L.) Merrill] genome studies, the high chromosome number (20) of the soybean plant relative to many other major crops has hindered the development of a high-resolution genomewide genetic map derived from a single population. Here, we report such a map, which was constructed in an F15 population derived from a cross between G. max and G. soja lines using indel polymorphisms detected via a G. soja genome resequencing. By targeting novel indel markers to marker-poor regions, all marker intervals were reduced to under 6 cM on a genome scale. Comparison of the Williams 82 soybean reference genome sequence and our genetic map indicated that marker orders of 26 regions were discrepant with each other. In addition, our comparison showed seven misplaced and two absent markers in the current Williams 82 assembly and six markers placed on the scaffolds that were not incorporated into the pseudomolecules. Then, we showed that, by determining the missing sequences located at the presumed beginning points of the five major discordant segments, these observed discordant regions are mostly errors in the Williams 82 assembly. Distributions of the recombination rates along the chromosomes were similar to those of other organisms. Genotyping of indel markers and genome resequencing of the two parental lines suggested that some marker-poor chromosomal regions may represent introgression regions, which appear to be prevalent in soybean. Given the even and dense distribution of markers, our genetic map can serve as a bridge between genomics research and breeding programs.
Collapse
Affiliation(s)
- Woo Kyu Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Chungbuk 363-883, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Yang L, Li D, Li Y, Gu X, Huang S, Garcia-Mas J, Weng Y. A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. BMC PLANT BIOLOGY 2013; 13:53. [PMID: 23531125 PMCID: PMC3626583 DOI: 10.1186/1471-2229-13-53] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 03/11/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. The availability of whole genome sequences provides an excellent opportunity for systematic identification and characterization of the nucleotide binding and leucine-rich repeat (NB-LRR) type R gene homolog (RGH) sequences in the genome. Cucumber has a very narrow genetic base making it difficult to construct high-density genetic maps. Development of a consensus map by synthesizing information from multiple segregating populations is a method of choice to increase marker density. As such, the objectives of the present study were to identify and characterize NB-LRR type RGHs, and to develop a high-density, integrated cucumber genetic-physical map anchored with RGH loci. RESULTS From the Gy14 draft genome, 70 NB-containing RGHs were identified and characterized. Most RGHs were in clusters with uneven distribution across seven chromosomes. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Phylogenetic analysis classified 58 RGHs into two clades: CNL and TNL. Comparative analysis revealed high-degree sequence homology and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. Fifty-four molecular markers were developed to delimit 67 of the 70 RGHs, which were integrated into a genetic map through linkage analysis. A 1,681-locus cucumber consensus map including 10 gene loci and spanning 730.0 cM in seven linkage groups was developed by integrating three component maps with a bin-mapping strategy. Physically, 308 scaffolds with 193.2 Mbp total DNA sequences were anchored onto this consensus map that covered 52.6% of the 367 Mbp cucumber genome. CONCLUSIONS Cucumber contains relatively few NB-LRR RGHs that are clustered and unevenly distributed in the genome. All RGHs seem to be transcribed and shared significant sequence homology and synteny with the melon genome suggesting conservation of these RGHs in the Cucumis lineage. The 1,681-locus consensus genetic-physical map developed and the RGHs identified and characterized herein are valuable genomics resources that may have many applications such as quantitative trait loci identification, map-based gene cloning, association mapping, marker-assisted selection, as well as assembly of a more complete cucumber genome.
Collapse
Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Dawei Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Yuhong Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100018, China
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100018, China
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, 08193, Spain
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| |
Collapse
|
39
|
Takada Y, Sasama H, Sayama T, Kikuchi A, Kato S, Ishimoto M, Tsukamoto C. Genetic and chemical analysis of a key biosynthetic step for soyasapogenol A, an aglycone of group A saponins that influence soymilk flavor. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:721-31. [PMID: 23229125 DOI: 10.1007/s00122-012-2013-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/24/2012] [Indexed: 06/01/2023]
Abstract
Although certain saponins in soybean seeds have been reported to have health benefits, group A acetyl saponins cause undesirable bitter and astringent tastes in soy products. Therefore, reduction or elimination of group A saponins is an important target for soybean breeders. A wide survey of cultivated and wild soybean germplasm identified a mutant line that lacked group A saponins. The absence of soyasapogenol A, a group A saponin aglycone, is controlled by a single recessive allele, sg-5 that mapped genetically near the SSR marker, Satt117, on soybean chromosome 15 (linkage group E). The locus is epistatic to Sg-1, which controls the terminal sugar variation on the C-22 sugar chain of soyasapogenol A, and allelic differences at this locus lead to changes in the amount of DDMP saponins and their derivatives group B and E products. These findings provide a new insight into the biosynthetic pathway of soybean saponins, and identify a genetic approach that can be applied to improve the quality of foods produced from soybean.
Collapse
Affiliation(s)
- Yoshitake Takada
- National Agricultural Research Organization (NARO) Western Region Agricultural Research Center, 1-3-1 Senyu, Zentsuji, Kagawa, 765-8508, Japan
| | | | | | | | | | | | | |
Collapse
|
40
|
Eskandari M, Cober ER, Rajcan I. Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:483-95. [PMID: 23192670 DOI: 10.1007/s00122-012-1995-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 10/06/2012] [Indexed: 05/20/2023]
Abstract
Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.
Collapse
Affiliation(s)
- Mehrzad Eskandari
- Department of Plant Agriculture, Crop Science Building, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | | | | |
Collapse
|
41
|
Duca M, Port A, Şestacova T, Siniauskaya M, Aksyonova E, Davydenko O. Microsatellite Marker Application in Sunflower ( Helianthus AnnuusL.) Fingerprinting. BIOTECHNOL BIOTEC EQ 2013. [DOI: 10.5504/bbeq.2013.0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
42
|
Roychowdhury R, Karmakar J, Karmakar J, Kumar Adak M, Dey N. Physio-Biochemical and Microsatellite Based Profiling of Lowland Rice (<i>Oryza sativa</i> L.) Landraces for Osmotic Stress Tolerance. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.412a3007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
43
|
Liu S, Kandoth PK, Warren SD, Yeckel G, Heinz R, Alden J, Yang C, Jamai A, El-Mellouki T, Juvale PS, Hill J, Baum TJ, Cianzio S, Whitham SA, Korkin D, Mitchum MG, Meksem K. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 2012; 492:256-60. [PMID: 23235880 DOI: 10.1038/nature11651] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022]
Abstract
Soybean (Glycine max (L.) Merr.) is an important crop that provides a sustainable source of protein and oil worldwide. Soybean cyst nematode (Heterodera glycines Ichinohe) is a microscopic roundworm that feeds on the roots of soybean and is a major constraint to soybean production. This nematode causes more than US$1 billion in yield losses annually in the United States alone, making it the most economically important pathogen on soybean. Although planting of resistant cultivars forms the core management strategy for this pathogen, nothing is known about the nature of resistance. Moreover, the increase in virulent populations of this parasite on most known resistance sources necessitates the development of novel approaches for control. Here we report the map-based cloning of a gene at the Rhg4 (for resistance to Heterodera glycines 4) locus, a major quantitative trait locus contributing to resistance to this pathogen. Mutation analysis, gene silencing and transgenic complementation confirm that the gene confers resistance. The gene encodes a serine hydroxymethyltransferase, an enzyme that is ubiquitous in nature and structurally conserved across kingdoms. The enzyme is responsible for interconversion of serine and glycine and is essential for cellular one-carbon metabolism. Alleles of Rhg4 conferring resistance or susceptibility differ by two genetic polymorphisms that alter a key regulatory property of the enzyme. Our discovery reveals an unprecedented plant resistance mechanism against a pathogen. The mechanistic knowledge of the resistance gene can be readily exploited to improve nematode resistance of soybean, an increasingly important global crop.
Collapse
Affiliation(s)
- Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Marone D, Laidò G, Gadaleta A, Colasuonno P, Ficco DBM, Giancaspro A, Giove S, Panio G, Russo MA, De Vita P, Cattivelli L, Papa R, Blanco A, Mastrangelo AM. A high-density consensus map of A and B wheat genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1619-38. [PMID: 22872151 PMCID: PMC3493672 DOI: 10.1007/s00122-012-1939-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/03/2012] [Indexed: 05/18/2023]
Abstract
A durum wheat consensus linkage map was developed by combining segregation data from six mapping populations. All of the crosses were derived from durum wheat cultivars, except for one accession of T. ssp. dicoccoides. The consensus map was composed of 1,898 loci arranged into 27 linkage groups covering all 14 chromosomes. The length of the integrated map and the average marker distance were 3,058.6 and 1.6 cM, respectively. The order of the loci was generally in agreement with respect to the individual maps and with previously published maps. When the consensus map was aligned to the deletion bin map, 493 markers were assigned to specific bins. Segregation distortion was found across many durum wheat chromosomes, with a higher frequency for the B genome. This high-density consensus map allowed the scanning of the genome for chromosomal rearrangements occurring during the wheat evolution. Translocations and inversions that were already known in literature were confirmed, and new putative rearrangements are proposed. The consensus map herein described provides a more complete coverage of the durum wheat genome compared with previously developed maps. It also represents a step forward in durum wheat genomics and an essential tool for further research and studies on evolution of the wheat genome.
Collapse
Affiliation(s)
- Daniela Marone
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Giovanni Laidò
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Agata Gadaleta
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | - Pasqualina Colasuonno
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | | | - Angelica Giancaspro
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | - Stefania Giove
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | - Giosué Panio
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Maria A. Russo
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | | | - Luigi Cattivelli
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
- CRA-Genomics Research Centre, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, PC Italy
| | - Roberto Papa
- CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
| | - Antonio Blanco
- Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola, 165/A, 70126 Bari, Italy
| | | |
Collapse
|
45
|
Cloutier S, Ragupathy R, Miranda E, Radovanovic N, Reimer E, Walichnowski A, Ward K, Rowland G, Duguid S, Banik M. Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1783-95. [PMID: 22890805 PMCID: PMC3493668 DOI: 10.1007/s00122-012-1953-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/21/2012] [Indexed: 05/06/2023]
Abstract
Three linkage maps of flax (Linum usitatissimum L.) were constructed from populations CDC Bethune/Macbeth, E1747/Viking and SP2047/UGG5-5 containing between 385 and 469 mapped markers each. The first consensus map of flax was constructed incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations. The 15 linkage group map corresponds to the haploid number of chromosomes of this species. The marker order of the consensus map was largely collinear in all three individual maps but a few local inversions and marker rearrangements spanning short intervals were observed. Segregation distortion was present in all linkage groups which contained 1-52 markers displaying non-Mendelian segregation. The total length of the consensus genetic map is 1,551 cM with a mean marker density of 2.0 cM. A total of 670 markers were anchored to 204 of the 416 fingerprinted contigs of the physical map corresponding to ~274 Mb or 74 % of the estimated flax genome size of 370 Mb. This high resolution consensus map will be a resource for comparative genomics, genome organization, evolution studies and anchoring of the whole genome shotgun sequence.
Collapse
Affiliation(s)
- Sylvie Cloutier
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 2012; 19:357-73. [PMID: 22864163 PMCID: PMC3473369 DOI: 10.1093/dnares/dss018] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.
Collapse
Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Isemura T, Kaga A, Tabata S, Somta P, Srinives P, Shimizu T, Jo U, Vaughan DA, Tomooka N. Construction of a genetic linkage map and genetic analysis of domestication related traits in mungbean (Vigna radiata). PLoS One 2012; 7:e41304. [PMID: 22876284 PMCID: PMC3410902 DOI: 10.1371/journal.pone.0041304] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 06/19/2012] [Indexed: 11/19/2022] Open
Abstract
The genetic differences between mungbean and its presumed wild ancestor were analyzed for domestication related traits by QTL mapping. A genetic linkage map of mungbean was constructed using 430 SSR and EST-SSR markers from mungbean and its related species, and all these markers were mapped onto 11 linkage groups spanning a total of 727.6 cM. The present mungbean map is the first map where the number of linkage groups coincided with the haploid chromosome number of mungbean. In total 105 QTLs and genes for 38 domestication related traits were identified. Compared with the situation in other Vigna crops, many linkage groups have played an important role in the domestication of mungbean. In particular the QTLs with high contribution were distributed on seven out of 11 linkage groups. In addition, a large number of QTLs with small contribution were found. The accumulation of many mutations with large and/or small contribution has contributed to the differentiation between wild and cultivated mungbean. The useful QTLs for seed size, pod dehiscence and pod maturity that have not been found in other Asian Vigna species were identified in mungbean, and these QTLs may play the important role as new gene resources for other Asian Vigna species. The results provide the foundation that will be useful for improvement of mungbean and related legumes.
Collapse
Affiliation(s)
- Takehisa Isemura
- Biodiversity Research Unit, Genetic Resources Center, National Institute of Agrobiological Science, Tsukuba, Ibaraki, Japan
| | - Akito Kaga
- Biodiversity Research Unit, Genetic Resources Center, National Institute of Agrobiological Science, Tsukuba, Ibaraki, Japan
| | - Satoshi Tabata
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Takehiko Shimizu
- Research Division 1 for Plants, Institute of Society for Techno-Innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Uken Jo
- Biodiversity Research Unit, Genetic Resources Center, National Institute of Agrobiological Science, Tsukuba, Ibaraki, Japan
| | - Duncan A. Vaughan
- Biodiversity Research Unit, Genetic Resources Center, National Institute of Agrobiological Science, Tsukuba, Ibaraki, Japan
| | - Norihiko Tomooka
- Biodiversity Research Unit, Genetic Resources Center, National Institute of Agrobiological Science, Tsukuba, Ibaraki, Japan
| |
Collapse
|
48
|
Rabbi IY, Kulembeka HP, Masumba E, Marri PR, Ferguson M. An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:329-42. [PMID: 22419105 DOI: 10.1007/s00122-012-1836-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 02/24/2012] [Indexed: 05/05/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important food security crops in the tropics and increasingly being adopted for agro-industrial processing. Genetic improvement of cassava can be enhanced through marker-assisted breeding. For this, appropriate genomic tools are required to dissect the genetic architecture of economically important traits. Here, a genome-wide SNP-based genetic map of cassava anchored in SSRs is presented. An outbreeder full-sib (F1) family was genotyped on two independent SNP assay platforms: an array of 1,536 SNPs on Illumina's GoldenGate platform was used to genotype a first batch of 60 F1. Of the 1,358 successfully converted SNPs, 600 which were polymorphic in at least one of the parents and was subsequently converted to KBiosciences' KASPar assay platform for genotyping 70 additional F1. High-precision genotyping of 163 informative SSRs using capillary electrophoresis was also carried out. Linkage analysis resulted in a final linkage map of 1,837 centi-Morgans (cM) containing 568 markers (434 SNPs and 134 SSRs) distributed across 19 linkage groups. The average distance between adjacent markers was 3.4 cM. About 94.2% of the mapped SNPs and SSRs have also been localized on scaffolds of version 4.1 assembly of the cassava draft genome sequence. This more saturated genetic linkage map of cassava that combines SSR and SNP markers should find several applications in the improvement of cassava including aligning scaffolds of the cassava genome sequence, genetic analyses of important agro-morphological traits, studying the linkage disequilibrium landscape and comparative genomics.
Collapse
Affiliation(s)
- Ismail Yusuf Rabbi
- International Institute of Tropical Agriculture, PMB 5320 Oyo Road, Ibadan, Nigeria.
| | | | | | | | | |
Collapse
|
49
|
Hudson CJ, Freeman JS, Kullan ARK, Petroli CD, Sansaloni CP, Kilian A, Detering F, Grattapaglia D, Potts BM, Myburg AA, Vaillancourt RE. A reference linkage map for Eucalyptus. BMC Genomics 2012; 13:240. [PMID: 22702473 PMCID: PMC3436727 DOI: 10.1186/1471-2164-13-240] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 06/04/2012] [Indexed: 01/26/2023] Open
Abstract
Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.
Collapse
Affiliation(s)
- Corey J Hudson
- School of Plant Science and CRC for Forestry, University of Tasmania, Private Bag 55 Hobart, Tasmania, 7001, Australia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Sayama T, Ono E, Takagi K, Takada Y, Horikawa M, Nakamoto Y, Hirose A, Sasama H, Ohashi M, Hasegawa H, Terakawa T, Kikuchi A, Kato S, Tatsuzaki N, Tsukamoto C, Ishimoto M. The Sg-1 glycosyltransferase locus regulates structural diversity of triterpenoid saponins of soybean. THE PLANT CELL 2012; 24:2123-38. [PMID: 22611180 PMCID: PMC3442591 DOI: 10.1105/tpc.111.095174] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Revised: 04/20/2012] [Accepted: 04/30/2012] [Indexed: 05/18/2023]
Abstract
Triterpene saponins are a diverse group of biologically functional products in plants. Saponins usually are glycosylated, which gives rise to a wide diversity of structures and functions. In the group A saponins of soybean (Glycine max), differences in the terminal sugar species located on the C-22 sugar chain of an aglycone core, soyasapogenol A, were observed to be under genetic control. Further genetic analyses and mapping revealed that the structural diversity of glycosylation was determined by multiple alleles of a single locus, Sg-1, and led to identification of a UDP-sugar-dependent glycosyltransferase gene (Glyma07g38460). Although their sequences are highly similar and both glycosylate the nonacetylated saponin A0-αg, the Sg-1(a) allele encodes the xylosyltransferase UGT73F4, whereas Sg-1(b) encodes the glucosyltransferase UGT73F2. Homology models and site-directed mutagenesis analyses showed that Ser-138 in Sg-1(a) and Gly-138 in Sg-1(b) proteins are crucial residues for their respective sugar donor specificities. Transgenic complementation tests followed by recombinant enzyme assays in vitro demonstrated that sg-1(0) is a loss-of-function allele of Sg-1. Considering that the terminal sugar species in the group A saponins are responsible for the strong bitterness and astringent aftertastes of soybean seeds, our findings herein provide useful tools to improve commercial properties of soybean products.
Collapse
Affiliation(s)
- Takashi Sayama
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Eiichiro Ono
- Institute for Plant Science, Suntory Business Expert Ltd., Shimamoto, Mishima, Osaka 618-8503, Japan
| | - Kyoko Takagi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Yoshitake Takada
- National Agricultural Research Center for Western Region, Zentsuji, Kagawa 765-8508, Japan
| | - Manabu Horikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Shimamoto, Mishima, Osaka 618-8503, Japan
| | - Yumi Nakamoto
- National Agricultural Research Center for Hokkaido Region, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Aya Hirose
- National Agricultural Research Center for Hokkaido Region, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | - Hiroko Sasama
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Mihoko Ohashi
- National Agricultural Research Center for Hokkaido Region, Toyohira, Sapporo, Hokkaido 062-8555, Japan
| | | | | | - Akio Kikuchi
- National Agricultural Research Center for Tohoku Region, Kariwano, Daisen, Akita 019-2112, Japan
| | - Shin Kato
- National Agricultural Research Center for Tohoku Region, Kariwano, Daisen, Akita 019-2112, Japan
| | - Nana Tatsuzaki
- Graduate School of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Chigen Tsukamoto
- Graduate School of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Masao Ishimoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| |
Collapse
|