Dr Li Li

Senior Scientist - Animal Genetics and Breeding Unit (AGBU)

Li Li

Phone: +61 2 6773 3790

Email: lli4@une.edu.au (lli4@une.edu.au)

Biography

After graduating from the Bachelor in Forestry at Jiangxi Agricultural University in 1992, Dr Li Li started his research career at Jiangxi Province Forestry Institute on a project involving the genetic improvement of Chinese fir, the most important forest plantation in southern China. After four years of hard but rewarding research work, he was motivated to pursue his career with higher degrees. Therefore, he went to study for his Master’s degree (majored in tree breeding, 1996-1998) and doctorate (majored in quantitative genetics in forestry, 1998-2001) at Nanjing Forestry University. In 2003, he conducted post-doctoral research at CSIRO (Canberra) on Australian Radiata pine breeding. In 2005, he was employed as a research fellow at the Animal Genetics and Breeding Unit (AGBU). Since then, his research interest has focused on applying the theory of quantitative genetics and breeding to improve productivity in livestock and plant production. Dr Li’s current research work is on three main areas. 1) Developing genetic evaluation systems to select for animal and plant industries; 2) Conducting genetic analysis of phenotypic and genomic data in plant and livestock species; 3) Applying animal breeding theory and methods to crop species by collaborating with crop breeders from the University of Western Australia (UWA).

Dr Li has engaged in developing, upgrading and, maintaining AGBU’s genetic evaluation systems for all species. This includes i) upgrading PIGBLUP software for pigs; ii) upgrading TREEPLAN software package from Version 2 to Version 3 for forestry; iii) developing innovative algorithms and software for calculation of the accuracy of genomic breeding values for BREEDPLAN (beef cattle) and Sheep Genetics (sheep). These genetic evaluation systems are used by thousands of breeders worldwide daily, resulting in significant increases in the profitability of respective industries.

Qualifications

2001 Doctor of Philosophy, Forest Quantitative Genetics, Nanjing Forestry University, Nanjing, PR China

1998 Master of Science, Forest Tree Improvement, Nanjing Forestry University, Nanjing, PR China

1992 Bachelor of Science, Forest Science, Jiangxi Agricultural University, Nanchang, PR China

Research Interests

  • Development of genetic evaluation software
  • Genetic parameters estimation
  • Genotype by environment interaction
  • Genetic analyses for threshold traits
  • Modeling of breeding programs by computer simulation
  • Linear mixed models for GWAS, BLUE and A/G/H-BLUP analyses

Research Achievements

  • Li was the leading computer programmer upgrading the cutting-edge genetic evaluation system -TREEPLAN (http://www.treebreeding.com/technology/treeplan) from Version 1 to Version 2 & 3. TREEPLAN has been used in tree and plant breeding by Tree Breeding Australia Ltd for Australian and international clients.
  • Li has played the leading role in upgrading and maintaining PIGBLUP software (http://agbu.une.edu.au/pig_genetics/pigblup.html), PIGBLUP has been used by pig breeders in Australia and overseas.
  • Li has been a key player in the AGBU team in developing algorithms and software for calculating the accuracy of genomic breeding values in large-scale datasets. The accuracy of the estimates of genetic merit is an important feature of the genetic evaluation systems AGBU develops and supports, including BREEDPLAN for beef (https://breedplan.une.edu.au/products/breedplan/) and MERINOSELECT and LAMBPLAN for sheep (https://www.sheepgenetics.org.au/). These systems are used by hundreds of breeders across several species in Australia and overseas. Li’s contribution to developing robust methods that can be applied rapidly on very large industry datasets has been vital in this step to using DNA information and maintaining the trust and confidence of the users.
  • In collaboration with plant breeders, Li has a strong interest in applying animal statistical models and methods, including multiple-trait animal models, optimum contribution selection, and selection index to plant species.

Publications

Refereed Journal Articles

Li, L; Gurman, P M; Swan, A A and Brown, D J (2021). Single-step genomic evaluation of lambing ease in Australian terminal sire breed sheep. Animal Production Science 61(18): 1990-1999 doi.org/10.1071/AN21257

Saradadevi, R; Mukankusi, C; Li, L; Amongi, W; Mbiu, J P; Raatz, B; Ariza, D; Beebe, S; Varshney, R K; Huttner, E; Kinghorn, B; Banks, R G; Rubyogo, J C; Siddique, K H M and Cowling, W A (2021). Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa. Plant Genome; 14(3): e20156 doi.org/10.1002/tpg2.20156

Moghaddar, N; Brown, D J; Swan, A A; Gurman, P M; Li, L and van der Werf, J H J (2021). Genomic prediction in a numerically small breed population using prioritized genetic variants from whole genome sequence data. Journal of Animal Breeding and Genetics, 139(1): 71-83. doi: 10.1111/jbg.12638

Tongsiri, S; Van der Werf, J H J; Li, L, Jeyaruban, M G; Wolcott, M L, Hermesch, S; Chormai, T (2020). Using random regression models to estimate genetic variation in growth pattern and its association with sexual maturity of Thai native chickens. British Poultry Science. 14:1-9.

Cowling, W; Li, L; Siddique, K, Banks, R; & Kinghorn, B (2019). Modeling crop breeding for global food security during climate change. Food and Energy Security, 8(2)

Guy, S Z Y; Li, L; Thomson, P C and Hermesch, S (2019). "Quantifying the health challenges in an Australian piggery using medication records for the definition of disease resilience." Journal of Animal Science 93: 4076-1089

Guy, S Z Y; Li, L; Thomson, P and Hermesch, S (2019). Reaction norm analysis of pig growth using environmental descriptors based on alternative traits. Journal of Animal Breeding and Genetics, 136, 153–167.

Tongsiri, S; Jeyaruban, G M; Hermesch, S; van der Werf, J; Li, L and Chormai, T (2019). Genetic parameters and inbreeding effects for production traits of Thai native chickens. Asian-Australasian journal of animal sciences, 32(7), 930–938. https://doi.org/10.5713/ajas.18.0690

Li, L; Brown, D J; Swan, A A and van der Werf, J H J (2018). Genetic parameters for faecal worm egg count at different ages in Australian sheep under natural challenge. Animal Production Science. 59(7):1201-1208.

Guy, S Z Y; Li, L; Thomson, P C and Hermesch, S (2017). Contemporary group estimates adjusted for climatic effects provide a finer definition of the unknown environmental challenges experienced by growing pigs. Journal of Animal Breeding and Genetics. 134 (6): 520-530

Cowling, W A; Li, L; Siddique, K H M; Henryon, M; Berg, P; Banks, R G and Kinghorn, B P (2017). Evolving gene banks: improving diverse populations of crop and exotic germplasm with optimal contribution selection, Journal of Experimental Botany 68(8):1927-1939.

Guy, S Z Y; Li, L;Thomson, P C and Hermesch, S (2017). Seasonal effects can be separated from other challenges in the pig environment using time series analysis. Animal Production Science, 57(12): 2463-2463.

Li, L and Hermesch, S (2016). Evaluation of sire by environment interactions for growth rate and backfat depth using reaction norm models in pigs. Journal of Animal Breeding and Genetics. 133: 429–440.

Li, L and Brown, D J (2016). Estimation of genetic parameters for lambing ease, birthweight and gestation length in Australian sheep. Animal Production Science. 56(5): 934–940.

Li, L, and Hermesch, S (2015). Environmental variation and breed sensitivity for growth rate and backfat depth in pigs. Animal Production Science. 56(1): 61-69.

Hermesch, S; Li, L; Doeschl-Wilson, A B and Gilbert, H (2015). Selection for productivity and robustness traits in pigs. Animal Production Science. 55(12): 1437–1447.

Kerr, R J; Li, L; Tier, B; Dutkowski, G W and McRae, T A (2012).  Use of the numerator relationship matrix in genetic analysis of autopolyploid species. Theoretical and Applied Genetics

Li, L and Wu, H (2005). Efficiency of Early Selection for Rotation-aged Growth and Wood Density Traits in Pinus radiate. Canadian Journal of Forest Research 35(8): 2019-2029.

Refereed Conference Proceedings/book chapters

Li, L; Gurman, P M; Swan, A A; Moghaddar, N and van der Werf, J H J (2021). Evaluating the benefits of including predictive markers in single step evaluation in sheep using cross-validation. Proceedings of the 24th Association for the Advancement of Animal Breeding and Genetics. 2-4 November, pp 200-203.

Gurman, P M; Li, L; Swan, A A; Moghaddar, N and van der Werf, J H J (2021). Multivariate analyses using two genomic relationship matrices to weight predictive SNP markers. Proceedings of the 24th Association for the Advancement of Animal Breeding and Genetics. 2-4 November, pp 135-138.

Moghaddar, N; Bunter, K L; Swan, A A; Li, L; Gurman, P M and van der Werf, J H J (2021) The effect of GDF9 on litter size in Australian sheep. Proceedings of the 24th Association for the Advancement of Animal Breeding and Genetics. 2-4 November, pp 238-241.

Gurman, P M; Li, L; Swan, A A; Moghaddar, N and van der Werf, J H J (2020). Partitioning of variance between multiple relationship matrices in BLUP analyses. Proceedings of the 6th International Conference of Quantitative Genetics, Two-week virtual conference 2020.

Mukankusi, C; Cowling, W A; Siddique, K H; Li, L; Kinghorn, B; Rubyogo, J C (2019). Diversity Breeding Program on Common Bean (Phaseolus vulgaris L.) Targeting Rapid Cooking and Iron and Zinc Biofortification. Proceedings, 36, 194.

Li, L; Swan, A A; Brown, D J and van der Werf, J H J (2019). Genotype by environment interaction in Australian maternal and terminal sheep. Proceedings of the 23st Association for the Advancement of Animal Breeding and Genetics, 23: 234-237.

Tongsiri, S; Jeyaruban, M G; Hermesch, S; van der Werf, J H J; Li, L and Chormai, T (2019). Genetic associations between early and late growth with sexual maturity in Thai native chickens. Proceedings of the 23nd Association for the Advancement of Animal Breeding and Genetics, 23: 163-167.

Guy, S Z Y; Li, L; Thomson, P C and Hermesch, S (2018). "Genetic parameters for health of the growing pig using medication records."  In Proceedings of the 11th World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand, 10-16 February.

Guy, S Z Y; Li, L; Thomson, P C and Hermesch, S (2018).  "Phenotypic, environmental and genetic associations between health and growth in the pig."  Proceedings of the 32nd Biennial Conference of the Australian Society of Animal Production (ASAP), Wagga Wagga, New South Wales, 2-4 July.

Brown, D J; Swan, A A; Boerner, V; Li, L; Gurman, P M; McMillan, A J; van der Werf, J H J; Chandler, H R; Tier, B and Banks, R G (2018). "Single-Step Genetic Evaluations in the Australian Sheep Industry."  In Proceedings of the 11th World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand, 10-16 February.

Cowling, W A and Li, L (2018). Turning the heat up on independent culling in crop breeding (book chapter).  In: Breeding Focus 2018: Reducing Heat Stress, Hermesch, S.(eds).  Armidale, Australia ).

Raman, H; Banks, R; Liu, S; Raman, R; Qiu, Y; McVittie, B.; Rohan, M; Li, L; Ferdosi, M; Menz, I and Cowling, W (2018). Genomic selection in global diversity pools - a new paradigm for prebreeding in canola. In the 20th Australian Research Assembly on Brassicas, in Perth 4th-6th September 2018.

Cowling, W; Chen, S and Li, L (2018). A model for pre-breeding canola for heat and drought tolerance during global climate change. In the 20th Australian Research Assembly on Brassicas, in Perth 4th-6th September 2018.

Li, L; Swan, A A and Tier, B (2017). Approximating the accuracy of single step EBVs. Proceedings of the 22nd Association for the Advancement of Animal Breeding and Genetics, 22: paper 20.

Guy, S Z Y; Harper, J; Li, L;Thomson, P C and Hermesch, S (2017). Extension of environmental descriptors used to analyze sire by environment interaction for growth of pigs. Proceedings of the 22nd Association for the Advancement of Animal Breeding and Genetics, 22: paper 54.

Tongsiri, S; Jeyaruban, M G; Hermesch, S; van der Werf, J H J; Li, L and Chormai, T (2017). Genetic parameters for body-weight traits of a native poultry breed in Thailand. Proceedings of the 22nd Association for the Advancement of Animal Breeding and Genetics, 22: paper 56.

Kerr, R J; Dutkowski, G W; Tier, B; Li, L and McRae, T A (2016). Investigating efficiency of selection using univariate and multivariate best linear unbiased predictors, International Unionof Forest Research Organizations (IUFRO) Genetics Conference in Rotorua NZ 14-18 March 2016.

Li, L; Swan, A A; Brown, D J and van der Werf, J H J (2015). Australian sheep breeding values for worm egg count retain predictive power across flocks in the presence of GxE. Proceedings of the 21st Association for the Advancement of Animal Breeding and Genetics, 21: 386-389.

Li, L and Hermesch, S (2013). Genotype by environment interactions for average daily gain using multiple-trait analyses in Australian pigs.  Proceedings of the 20th Association for the Advancement of Animal Breeding and Genetics, 20: 323-326.

Li, L; Brown, D Jand Gill, J S (2013).  Genetic parameters for body weight, carcass and wool traits in Dohne Merino.  Proceedings of the 20th Association for the Advancement of Animal Breeding and Genetics, 20: 241-244.

Hermesch, S and Li, L (2013).  The effect of dam parity on growth of pigs differs between herds. Proceedings of the 14th Biennial Conference of the Australian Pig Science Association (APSA), Melbourne, Victoria, November 24-27.  p.53.

Hermesch, S and Li, L (2013). Variability in growth and backfat of finisher pigs grown in superior and poor environments. Proceedings of the 14th Biennial Conference of the Australian Pig Science Association (APSA), Melbourne, Victoria, November 24-27.  p.214.

Li, L and Hermesch, S (2012).  Genotypes differ in their response to variation in environments experienced by pigs on farm.  In: Pig Genetics Workshop Notes 2012, Hermesch, S. and Dobos, K. J. (eds).  Armidale, Australia, pp. 53-60.

Kerr, R J; Dutkowski, G W; Li, L; McRae, T A; Novy, R; Schneider, B and Tier, B (2009).  Integrated genetic analysis for potato improvement. Proceedings of 2009 14th Australasian Plant Breeding Conference (APBC) and 11th Congress of the Society for the Advancement of Breeding Research in Asia and Oceana (SABRAO) Contemporary Crop Improvement: A Tropical View. Cairns, Queensland, Australia, 10-14 August.

Memberships

Member - Association for the Advancement of Breeding and Genetics (AAABG)

Further Information

Other Interests

I love to play table tennis and badminton.

Memberships

Member - Association for the Advancement of Breeding and Genetics (AAABG)