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Kunta S, Chu Y, Levy Y, Harel A, Abbo S, Ozias-Akins P, Hovav R. Identification of a major locus for flowering pattern sheds light on plant architecture diversification in cultivated peanut. Theor Appl Genet 2022; 135:1767-1777. [PMID: 35260930 DOI: 10.1007/s00122-022-04068-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
A major gene controls flowering pattern in peanut, possibly encoding a TFL1-like. It was subjected to gain/loss events of a deletion and changes in mRNA expression levels, partly explaining the evolution of flowering pattern in Arachis. Flowering pattern (FP) is a major characteristic differentiating the two subspecies of cultivated peanut (Arachis hypogaea L.). Subsp. fastigiata possessing flowers on the mainstem (MSF) and a sequential FP, whereas subsp. hypogaea lacks MSF and exhibits an alternate FP. FP is considered the main contributor to plant adaptability, and evidence indicates that its diversification occurred during the several thousand years of domestication. However, the genetic mechanism that controls FP in peanut is unknown. We investigated the genetics of FP in a recombinant inbred population, derivatives of an A. hypogaea by A. fastigiata cross. Lines segregated 1:1 for FP, indicating a single gene effect. Using Axiom_Arachis2 SNP-array, FP was mapped to a small segment in chromosome B02, wherein a Terminal Flowering 1-like (AhTFL1) gene with a 1492 bp deletion was found in the fastigiata line, leading to a truncated protein. Remapping FP in the RIL population with the AhTFL1 indel as a marker increased the LOD score from 53.3 to 158.8 with no recombination in the RIL population. The same indel was found co-segregating with the phenotype in two independent EMS-mutagenized M2 families, suggesting a hotspot for gene conversion. Also, AhTFL1 was significantly less expressed in the fastigiata line compared to hypogaea and in flowering than non-flowering branches. Sequence analysis of the AhTFL1 in peanut world collections indicated significant conservation, supporting the putative role of AhTFL1 in peanut speciation during domestication and modern cultivation.
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Affiliation(s)
- Srinivas Kunta
- Department of Field Crops, Institute of Plant Sciences, Agriculture Research Organization-The Volcani Institute, HaMakkabbim Road, POB 15159, 7505101, Rishon LeZion, Israel
- Faculty of Agricultural, Food and the Environmental Quality Sciences, The Hebrew University of Jerusalem, POB 12, 7610001, Rehovot, Israel
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Yael Levy
- Department of Field Crops, Institute of Plant Sciences, Agriculture Research Organization-The Volcani Institute, HaMakkabbim Road, POB 15159, 7505101, Rishon LeZion, Israel
| | - Arye Harel
- Department of Field Crops, Institute of Plant Sciences, Agriculture Research Organization-The Volcani Institute, HaMakkabbim Road, POB 15159, 7505101, Rishon LeZion, Israel
| | - Shahal Abbo
- Faculty of Agricultural, Food and the Environmental Quality Sciences, The Hebrew University of Jerusalem, POB 12, 7610001, Rehovot, Israel
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Ran Hovav
- Department of Field Crops, Institute of Plant Sciences, Agriculture Research Organization-The Volcani Institute, HaMakkabbim Road, POB 15159, 7505101, Rishon LeZion, Israel.
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Kunta S, Agmon S, Chedvat I, Levy Y, Chu Y, Ozias-Akins P, Hovav R. Identification of consistent QTL for time to maturation in Virginia-type Peanut (Arachis hypogaea L.). BMC Plant Biol 2021; 21:186. [PMID: 33874903 PMCID: PMC8054412 DOI: 10.1186/s12870-021-02951-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Time-to-maturation (TTM) is an important trait contributing to adaptability, yield and quality in peanut (Arachis hypogaea L). Virginia market-type peanut belongs to the late-maturing A. hypogaea subspecies with considerable variation in TTM within this market type. Consequently, planting and harvesting schedule of peanut cultivars, including Virginia market-type, need to be optimized to maximize yield and grade. Little is known regarding the genetic control of TTM in peanut due to the challenge of phenotyping and limited DNA polymorphism. Here, we investigated the genetic control of TTM within the Virginia market-type peanut using a SNP-based high-density genetic map. A recombinant inbred line (RIL) population, derived from a cross between two Virginia-type cultivars 'Hanoch' and 'Harari' with contrasting TTM (12-15 days on multi-years observations), was phenotyped in the field for 2 years following a randomized complete block design. TTM was estimated by maturity index (MI). Other agronomic traits like harvest index (HI), branching habit (BH) and shelling percentage (SP) were recorded as well. RESULTS MI was highly segregated in the population, with 13.3-70.9% and 28.4-80.2% in years 2018 and 2019. The constructed genetic map included 1833 SNP markers distributed on 24 linkage groups, covering a total map distance of 1773.5 cM corresponding to 20 chromosomes on the tetraploid peanut genome with 1.6 cM mean distance between the adjacent markers. Thirty QTL were identified for all measured traits. Among the four QTL regions for MI, two consistent QTL regions (qMIA04a,b and qMIB03a,b) were identified on chromosomes A04 (118680323-125,599,371; 6.9Mbp) and B03 (2839591-4,674,238; 1.8Mbp), with LOD values of 5.33-6.45 and 5-5.35 which explained phenotypic variation of 9.9-11.9% and 9.3-9.9%, respectively. QTL for HI were found to share the same loci as MI on chromosomes B03, B05, and B06, demonstrating the possible pleiotropic effect of HI on TTM. Significant but smaller effects on MI were detected for BH, pod yield and SP. CONCLUSIONS This study identified consistent QTL regions conditioning TTM for Virginia market-type peanut. The information and materials generated here can be used to further develop molecular markers to select peanut idiotypes suitable for diverse growth environments.
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Affiliation(s)
- Srinivas Kunta
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
- Faculty of Agricultural, Food and The Environmental Quality Sciences, The Hebrew University of Jerusalem, POB 12, 76100, Rehovot, Israel
| | - Sara Agmon
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
| | - Ilan Chedvat
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
| | - Yael Levy
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, 31793, USA
| | - Ran Hovav
- Department of Field Crops, Agriculture Research Organization-The Volcani Center, Institute of Plant Sciences, HaMakkabbim Road, P. O. Box 15159, 7505101, Rishon LeZiyyon, Israel.
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Frankin S, Kunta S, Abbo S, Sela H, Goldberg BZ, Bonfil DJ, Levy AA, Avivi-Ragolsky N, Nashef K, Roychowdhury R, Faraj T, Lifshitz D, Mayzlish-Gati E, Ben-David R. The Israeli-Palestinian wheat landraces collection: restoration and characterization of lost genetic diversity. J Sci Food Agric 2020; 100:4083-4092. [PMID: 31141162 DOI: 10.1002/jsfa.9822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/23/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND For over a century, genetic diversity of wheat worldwide was eroded by continual selection for high yields and industrial demands. Wheat landraces cultivated in Israel and Palestine demonstrate high genetic diversity and a potentially wide repertoire of adaptive alleles. While most Israeli-Palestinian wheat landraces were lost in the transition to 'Green Revolution' semi-dwarf varieties, some germplasm collections made at the beginning of the 20th century survived in gene banks and private collections worldwide. However, fragmentation and poor conservation place this unique genetic resource at a high risk of genetic erosion. Herein, we describe a long-term initiative to restore, conserve, and characterize a collection of Israeli and Palestinian wheat landraces (IPLR). RESULTS We report on (i) the IPLR construction (n = 932), (ii) the historical and agronomic context to this collection, (iii) the characterization and assessment of the IPLR's genetic diversity, and (iv) a data comparison from two distinct subcollections within IPLR: a collection made by N. Vavilov in 1926 (IPLR-VIR) and a later one (1979-1981) made by Y. Mattatia (IPLR-M). Though conducted in the same eco-geographic space, these two collections were subjected to considerably different conservation pathways. IPLR-M, which underwent only one propagation cycle, demonstrated marked genetic and phenotypic variability (within and between accessions) in comparison with IPLR-VIR, which had been regularly regenerated over ∼90 years. CONCLUSION We postulate that long-term ex situ conservation involving human and genotype × environment selection may significantly reduce accession heterogeneity and allelic diversity. Results are further discussed in a broader context of pre-breeding and conservation. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Sivan Frankin
- Department of Vegetables and Field Crop, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Srinivas Kunta
- Department of Vegetables and Field Crop, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shahal Abbo
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Hanan Sela
- Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv, Israel
| | | | - David J Bonfil
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization, Gilat Research Center, M.P. Negev, Israel
| | - Avraham A Levy
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Avivi-Ragolsky
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Kamal Nashef
- Department of Vegetables and Field Crop, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Rajib Roychowdhury
- Department of Vegetables and Field Crop, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Tomer Faraj
- Israel Gene Bank, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dikla Lifshitz
- Israel Gene Bank, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Einav Mayzlish-Gati
- Israel Gene Bank, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Roi Ben-David
- Department of Vegetables and Field Crop, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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