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Lake L, Hayes JE, Ortega Martinez R, Weller JL, Javid M, Butler JB, James LE, Gimenez R, Dreccer MF, French R, Sadras VO. Genetics of phenological development and implications for seed yield in lentil. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4772-4783. [PMID: 38712747 DOI: 10.1093/jxb/erae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/05/2024] [Indexed: 05/08/2024]
Abstract
Understanding phenology, its genetics and agronomic consequences, is critical for crop adaptation. Here we aim to (i) characterize lentil response to photoperiod with a focus on five loci: the lentil ELF3 orthologue Sn, two loci linked to clusters of lentil FT orthologues, and two loci without candidates in chromosomes 2 and 5 (Experiment 1: 36 lines, short and long days in a phytotron), and (ii) establish the phenology-yield relationship (Experiment 2: 25 lines, 11 field environments). A vintage perspective, where we quantify time trends in phenotype over three decades of breeding, links both experiments. Yield increased linearly from older to newer varieties at 29 kg ha-1 year-1 or 1.5% year-1, correlated negatively with flowering time in both winter- and summer-rainfall regimes, and decoupled from biomass in favourable environments. Time to flowering shortened from older to newer varieties at -0.56% year-1 in the field, and -0.42% year-1 (short days) and -0.99% year-1 (long days) in the phytotron. Early-flowering lines of diverse origin carried multiple early alleles for the five loci, indicating that at least some of these loci affect phenology additively. Current germplasm primarily features the early-flowering haplotype for an FTb cluster region, hence the potential to increase phenological diversity with yield implications.
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Affiliation(s)
- Lachlan Lake
- South Australian Research and Development Institute, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, Australia
- College of Science and Engineering, Flinders University, Australia
| | - Julie E Hayes
- School of Agriculture, Food and Wine, The University of Adelaide, Australia
| | - Raul Ortega Martinez
- School of Natural Sciences, University of Tasmania, Sandy Bay Campus, Hobart, Tasmania, Australia
| | - Jim L Weller
- School of Natural Sciences, University of Tasmania, Sandy Bay Campus, Hobart, Tasmania, Australia
| | - Muhammad Javid
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
| | - Jacob B Butler
- School of Natural Sciences, University of Tasmania, Sandy Bay Campus, Hobart, Tasmania, Australia
| | - Laura E James
- School of Natural Sciences, University of Tasmania, Sandy Bay Campus, Hobart, Tasmania, Australia
| | - Raul Gimenez
- South Australian Research and Development Institute, Australia
- School of Natural Sciences, University of Tasmania, Sandy Bay Campus, Hobart, Tasmania, Australia
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - M Fernanda Dreccer
- Commonwealth Scientific and Industrial Research Organisation, Queensland, Australia
| | - Robert French
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
| | - Victor O Sadras
- South Australian Research and Development Institute, Australia
- School of Agriculture, Food and Wine, The University of Adelaide, Australia
- College of Science and Engineering, Flinders University, Australia
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Gebremedhin A, Li Y, Shunmugam ASK, Sudheesh S, Valipour-Kahrood H, Hayden MJ, Rosewarne GM, Kaur S. Genomic selection for target traits in the Australian lentil breeding program. FRONTIERS IN PLANT SCIENCE 2024; 14:1284781. [PMID: 38235201 PMCID: PMC10791954 DOI: 10.3389/fpls.2023.1284781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/07/2023] [Indexed: 01/19/2024]
Abstract
Genomic selection (GS) uses associations between markers and phenotypes to predict the breeding values of individuals. It can be applied early in the breeding cycle to reduce the cross-to-cross generation interval and thereby increase genetic gain per unit of time. The development of cost-effective, high-throughput genotyping platforms has revolutionized plant breeding programs by enabling the implementation of GS at the scale required to achieve impact. As a result, GS is becoming routine in plant breeding, even in minor crops such as pulses. Here we examined 2,081 breeding lines from Agriculture Victoria's national lentil breeding program for a range of target traits including grain yield, ascochyta blight resistance, botrytis grey mould resistance, salinity and boron stress tolerance, 100-grain weight, seed size index and protein content. A broad range of narrow-sense heritabilities was observed across these traits (0.24-0.66). Genomic prediction models were developed based on 64,781 genome-wide SNPs using Bayesian methodology and genomic estimated breeding values (GEBVs) were calculated. Forward cross-validation was applied to examine the prediction accuracy of GS for these targeted traits. The accuracy of GEBVs was consistently higher (0.34-0.83) than BLUP estimated breeding values (EBVs) (0.22-0.54), indicating a higher expected rate of genetic gain with GS. GS-led parental selection using early generation breeding materials also resulted in higher genetic gain compared to BLUP-based selection performed using later generation breeding lines. Our results show that implementing GS in lentil breeding will fast track the development of high-yielding cultivars with increased resistance to biotic and abiotic stresses, as well as improved seed quality traits.
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Affiliation(s)
- Alem Gebremedhin
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Yongjun Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | | | - Shimna Sudheesh
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | | | - Matthew J. Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Maphosa L, Preston A, Richards MF. Effect of Sowing Date and Environment on Phenology, Growth and Yield of Lentil ( Lens culinaris Medikus.) Genotypes. PLANTS (BASEL, SWITZERLAND) 2023; 12:474. [PMID: 36771562 PMCID: PMC9922022 DOI: 10.3390/plants12030474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/20/2022] [Accepted: 12/06/2022] [Indexed: 06/18/2023]
Abstract
Lentil, an important pulse crop in Australia, is sown soon after the onset of autumn rains and grows mainly under rainfed conditions. This study examined lentil phenological development, growth and grain yield under different sowing dates and environments in New South Wales (NSW). Eight lentil varieties were phenotyped over two years and four sowing times in southern NSW (Leeton, Wagga Wagga and Yanco (one year)) and central western NSW (Trangie). Time of sowing affected important agronomic traits, with a delay in sowing decreasing time to flowering and podding, biomass accumulation, plant height and position of bottom pod. Sowing earlier or later than optimum decreased grain yield. Yield was mainly determined by the number of pods and seeds per plant, with minimal impact from seed weight. Overall, yields were higher in favorable environments such Leeton experiment which received more water compared to the other sites which received less water. Averaged across sowing dates, the slower maturing PBA Greenfield was lower yielding whilst fast maturing varieties such as PBA Bolt and PBA Blitz yielded higher. PBA Jumbo2 is less sensitive to environmental interaction and thus broadly adapted to the diverse environments. Optimum sowing time was identified as the end of April to mid-May.
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Tefera AT, O’Leary GJ, Thayalakumaran T, Rao S, Silva-Perez V, Shunmugam ASK, Armstrong R, Rosewarne GM. Identification of agro-physiological traits of lentil that reduce risks of drought. FRONTIERS IN PLANT SCIENCE 2022; 13:1019491. [PMID: 36352869 PMCID: PMC9637959 DOI: 10.3389/fpls.2022.1019491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Ideotype breeding is an essential approach for selection of desired combination of plant traits for testing in crop growth model for potential yield gain in specific environments and management practices. Here we parameterized plant traits for untested lentil cultivars for the APSIM-lentil model in phenology, biomass, and seed yield. We then tested these against independent data and applied the model in an extrapolated analysis (i) to assess the impact of drought on productivity across different rainfall environments; (ii) to identify impactful plant traits and (iii) to design new lentil ideotypes with a combination of desirable traits that mitigate the impact of drought, in the context of various agronomic practices across a wide range of production environments. Desirable phenological and physiological traits related to yield were identified with RUE having the greatest effect on yield followed by HI rate. Leaf size significantly affected seed yield (p< 0.05) more than phenological phases. The physiological traits were integrated into four ideotype designs applied to two baseline cultivars (PBA Hallmark XT and PBA Jumbo2) providing eight ideotypes. We identified a combination of genetic traits that promises a yield advantage of around 10% against our current cultivars PBA Hallmark XT and PBA Jumbo2. Under drought conditions, our ideotypes achieved 5 to 25% yield advantages without stubble and 20 to 40% yield advantages with stubble residues. This shows the importance of genetic screening under realistic production conditions (e.g., stubble retention in particular environments). Such screening is aided by the employment of biophysical models that incorporate both genetic and agronomic variables that focus on successful traits in combination, to reduce the impact of drought in the development of new cultivars for various environments. Stubble retention was found to be a major agronomic contributor to high yield in water-limiting environments and this contribution declined with increasing growing season rainfall. In mid- and high-rainfall environments, the key drivers of yield were time of sowing, physiological traits and soil type. Overall, the agronomic practices, namely, early sowing, residue retention and narrow row spacing deceased the impact of drought when combined with improved physiological traits of the ideotypes based on long term climate data.
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Affiliation(s)
| | - Garry J. O’Leary
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC, Australia
| | - Thabo Thayalakumaran
- Agriculture Victoria Research, Centre for Agri Bioscience, Melbourne, VIC, Australia
| | - Shiwangni Rao
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
| | | | | | - Roger Armstrong
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Garry M. Rosewarne
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC, Australia
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Silva-Perez V, Shunmugam ASK, Rao S, Cossani CM, Tefera AT, Fitzgerald GJ, Armstrong R, Rosewarne GM. Breeding has selected for architectural and photosynthetic traits in lentils. FRONTIERS IN PLANT SCIENCE 2022; 13:925987. [PMID: 36092438 PMCID: PMC9453451 DOI: 10.3389/fpls.2022.925987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Genetic progress in seed yield in lentils (Lens culinaris Medik) has increased by 1.1% per year in Australia over the past 27 years. Knowing which plant traits have changed through breeding during this time can give important insights as to how lentil yield has increased. This study aims to identify morphological and physiological traits that were directly or indirectly selected between 1993 and 2020 in the Australian lentil breeding program using 2 years of experimental data. Major changes occurred in plant architecture during this period. Divergent selection has seen the release of varieties that have sprawling to very upright types of canopies. Despite this genetic diversity in recently released varieties, there is an overall tendency of recently released varieties having increased plant height and leaf size with reduced number of branches. Increased light interception was positively correlated with year of release (YOR) and yield, and likely results from indirect selection of yield and taller plant types. There is an indication that recently released varieties have lower CO2 assimilation rate, stomatal conductance and canopy temperature depression (CTD) at high ambient temperatures (~30°C). Understanding lentil physiology will assist in identifying traits to increase yield in a changing climate with extreme weather events.
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Affiliation(s)
| | | | | | - C. Mariano Cossani
- School of Agriculture, Food and Wine, South Australian Research and Development Institute, The University of Adelaide, Urrbrae, SA, Australia
| | | | - Glenn J. Fitzgerald
- Agriculture Victoria, Horsham, VIC, Australia
- Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Roger Armstrong
- Agriculture Victoria, Horsham, VIC, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, Australia
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Sharwood RE, Quick WP, Sargent D, Estavillo GM, Silva-Perez V, Furbank RT. Mining for allelic gold: finding genetic variation in photosynthetic traits in crops and wild relatives. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3085-3108. [PMID: 35274686 DOI: 10.1093/jxb/erac081] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Improvement of photosynthetic traits in crops to increase yield potential and crop resilience has recently become a major breeding target. Synthetic biology and genetic technologies offer unparalleled opportunities to create new genetics for photosynthetic traits driven by existing fundamental knowledge. However, large 'gene bank' collections of germplasm comprising historical collections of crop species and their relatives offer a wealth of opportunities to find novel allelic variation in the key steps of photosynthesis, to identify new mechanisms and to accelerate genetic progress in crop breeding programmes. Here we explore the available genetic resources in food and fibre crops, strategies to selectively target allelic variation in genes underpinning key photosynthetic processes, and deployment of this variation via gene editing in modern elite material.
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Affiliation(s)
- Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - W Paul Quick
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Demi Sargent
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | | | | | - Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, Canberra, ACT, Australia
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Jha TB. Critical review on karyotype diversity in lentil based on classical and molecular cytogenetics. Mol Biol Rep 2022; 49:9699-9714. [PMID: 35461437 DOI: 10.1007/s11033-022-07441-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
Abstract
Lentil is an annual protein rich valuable edible crop with only one cultivated and six wild taxa. Keeping in mind its narrow gene pool, the genus deserves critical assessment of genomic diversity at the chromosomal level. Genetic diversity represents the heritable variation within and between populations of organisms. Over the decades classical and molecular cytogenetics have played an immense role in the field of crop improvement. Lentil, though grown in different countries, country-wise chromosomal information is inadequate. Critical evaluation of more than seven decades chromosomal information has revealed unique karyotype diversity within the landraces of different countries. Application of fluorescent banding and fluorescent in situ hybridization (FISH) has helped to segregate cultivars based on cultivar specific chromosomal markers and landmarks. Selection of cultivated and wild cultivars based on qualitative and diseases related morpho-traits and new information from this critical review especially on molecular cytogenetics may provide more options for crop improvement. More research in the field of molecular cytogenetics from country specific species and cultivars are needed to enrich the repository of gene pool. Alien gene introgression from extended gene pool through the advanced genomics and biotechnological tools could facilitate the path of sustainable improvement of this crop.
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Affiliation(s)
- Timir Baran Jha
- Department of Botany, Maulana Azad College, Rafi Ahmed Kidwai Road, Kolkata, West Bengal, 700013, India.
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