Person: Hearne, S.
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Hearne
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S.
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Hearne, S.
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0000-0003-2015-2450 8 results
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- DNNGP, a deep neural network-based method for genomic prediction using multi-omics data in plants(Cell Press, 2023) Wang, K.; Abid, M.A.; Rasheed, A.; Crossa, J.; Hearne, S.; Huihui Li
Publication - A comparison of the adoption of genomic selection across different breeding institutions(Frontiers, 2021) Gholami, M.; Wimmer, V.; Sansaloni, C.; Petroli, C.; Hearne, S.; Covarrubias, E.; Rensing, S.; Heise, J.; Pérez-Rodríguez, P.; Dreisigacker, S.; Crossa, J.; Martini, J.W.R.
Publication - Opportunities and challenges of predictive approaches for harnessing the potential of genetic resources(Frontiers, 2021) Martini, J.W.R.; Molnar, T.L.; Crossa, J.; Hearne, S.; Pixley, K.V.
Publication - Evaluation of genomic selection training population designs and genotyping strategies in plant breeding programs using simulation(CSSA, 2014) Hickey, J.; Dreisigacker, S.; Crossa, J.; Hearne, S.; Babu, R.; Prasanna, B.M.; Grondona, M.; Zambelli, A.; Windhausen, V.S.; Mathews, K.L.; Gorjanc, G.
Publication - The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections(BioMed Central, 2019) Franco, J.; Crossa, J.; Jiafa Chen; Hearne, S.Background: Germplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider collection. A relevant question is whether it is necessary to develop completely independent germplasm samples or it is possible to select nested sets from a pre-defined core set panel not from the whole collection. We used data from 15,384, maize landraces stored in the CIMMYT germplasm bank to study the impact on 8 diversity criteria and the sample representativeness of: (1) two core selection strategies, a statistical sampling (DM), or a numerical maximization method (CH); (2) selecting samples of varying sizes; and (3) selecting samples of different sizes independently of each other or in a nested manner. Results: Sample sizes greater than 10% of the whole population size retained more than 75% of the polymorphic markers for all selection strategies and types of sample; lower sample sizes showed more variability (instability) among repetitions; the strongest effect of sample size was observed on the CH-independent combination. Independent and nested samples showed similar performance for all the criteria for the DM method, but there were differences between them for the CH method. The DM method achieved better approximations to the known values in the population than the CH method; 2-d multidimensional scaling plots of the collection and samples highlighted tendency of sample selection towards the extremes of diversity in the CH method, compared with sampling more representative of the overall genotypic distribution of diversity under the DM method. Conclusions: The use of core subsets of size greater than or equal to 10% of the whole collection satisfied well the requirement of representativeness and diversity. Nested samples showed similar diversity and representativeness characteristics as independent samples offering a cost effective method of sample definition for germplasm banks. For most criteria assessed the DM method achieved better approximations to the known values in the whole population than the CH method, that is, it generated more statistically representative samples from collections.
Publication - Genetic gains in grain yield of a maize population improved through marker assisted recurrent selection under stress and non-stress conditions in West Africa(Frontiers, 2017) Abdulmalik, R.O.; Menkir, A.; Meseka, S.; Unachukwu, N.; Ado, S.; Olarewaju, J.D.; Aba, D. A.; Hearne, S.; Crossa, J.; Gedil, M.Marker-assisted recurrent selection (MARS) is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S1 lines derived from the original (C0) and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS) and well-watered (WW) conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S1 lines each derived from the four cycles (C0, C1, C2, C3) were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga, improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S1 lines from 114 in C0 to 124 in C3. The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved maize inbred lines.
Publication - Genetic gains in yield and yield related traits under drought stress and favorable environments in a maize population improved using marker assisted recurrent selection(Frontiers, 2017) Bankole, F.; Menkir, A.; Olaoye, G.; Crossa, J.; Hearne, S.; Unachukwu, N.; Gedil, M.The objective of marker assisted recurrent selection (MARS) is to increase the frequency of favorable marker alleles in a population before inbred line extraction. This approach was used to improve drought tolerance and grain yield (GY) in a biparental cross of two elite drought tolerant lines. The testcrosses of randomly selected 50 S1 lines from each of the three selection cycles (C0, C1, C2) of the MARS population, parental testcrosses and the cross between the two parents (F1) were evaluated under drought stress (DS) and well watered (WW) well as under rainfed conditions to determine genetic gains in GY and other agronomic traits. Also, the S1 lines derived from each selection types were genotyped with single nucleotide polymorphism (SNP) markers. Testcrosses derived from C2 produced significantly higher grain field under DS than those derived from C0 with a relative genetic gain of 7% per cycle. Also, the testcrosses of S1 lines from C2 showed an average genetic gain of 1% per cycle under WW condition and 3% per cycle under rainfed condition. Molecular analysis revealed that the frequency of favorable marker alleles increased from 0.510 at C0 to 0.515 at C2, while the effective number of alleles (Ne) per locus decreased from C0 (1.93) to C2 (1.87). Our results underscore the effectiveness of MARS for improvement of GY under DS condition.
Publication - Identification of drought, heat, and combined drought and heat tolerant donors in maize(Crop Science Society of America (CSSA), 2013) Cairns, J.E.; Crossa, J.; Zaidi, P.; Grudloyma, P.; Sanchez, C.; Araus, J.L.; Thaitad, S.; Makumbi, D.; Magorokosho, C.; Banziger, M.; Menkir, A.; Hearne, S.; Atlin, G.Low maize (Zea maysL.) yields and the impacts of climate change on maize production highlight the need to improve yields in eastern and southern Africa. Climate projections suggest higher temperatures within drought-prone areas. Research in model species suggests that tolerance to combined drought and heat stress is genetically distinct from tolerance to either stress alone, but this has not been confirmed in maize. In this study we evaluated 300 maize inbred lines testcrossed to CML539. Experiments were conducted under optimal conditions, reproductive stage drought stress, heat stress, and combined drought and heat stress. Lines with high levels of tolerance to drought and combined drought and heat stress were identified. Significant genotype × trial interaction and very large plot residuals were observed; consequently, the repeatability of individual managed stress trials was low. Tolerance to combined drought and heat stress in maize was genetically distinct from tolerance to individual stresses, and tolerance to either stress alone did not confer tolerance to combined drought and heat stress. This finding has major implications for maize drought breeding. Many current drought donors and key inbreds used in widely grown African hybrids were susceptible to drought stress at elevated temperatures. Several donors tolerant to drought and combined drought and heat stress, notably La Posta Sequia C7-F64-2-6-2-2 and DTPYC9-F46-1-2-1-2, need to be incorporated into maize breeding pipelines.
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