|
References
Alexander D H, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome research, 19: 1655-1664.
Baloch F S, Altaf M T, Liaqat W, Bedir M, Nadeem M A, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I. 2023. Recent advancements in the breeding of sorghum crop: Current status and future strategies for marker-assisted breeding. Frontiers in Genetics, 14, 1150616.
Baye W, Xie Q, Xie P. 2022. Genetic architecture of grain yield-related traits in sorghum and maize. International Journal of Molecular Sciences, 23, 2405.
Bekele W A, Wieckhorst S, Friedt W, Snowdon R J. 2013. High-throughput genomics in sorghum: From whole‐genome resequencing to a SNP screening array. Plant Biotechnology Journal, 11, 1112-1125.
Boyles R E, Brenton Z W, Kresovich S. 2019. Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments. The Plant Journal, 97, 19-39.
Chao K, Wu C, Li J, Wang W, Wang B, Li Q. 2022. Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat landrace Wudubaijian in multi-environment trials. Journal of Integrative Agriculture, 21, 2305–2318.
Chen B R, Wang C Y, Wang G P, Zhu Z X, Xu N, Shi G S, Yu M, Wang N, Li J H, Hou J M. 2019. Genome-wide association study for starch content and constitution in sorghum (Sorghum bicolor (L.) Moench). Journal of Integrative Agriculture, 18, 2446-2456.
Chen H, Xie W, He H, Yu H, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X, Zhou F, Deng X W, Zhang Q. 2014. A high-density SNP genotyping array for rice biology and molecular breeding. Molecular Plant, 7, 541–553.
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34, 17, i884–i890.
Danecek P, Auton A, Abecasis G, Albers C A, Banks E, DePristo M A, Handsaker R E, Lunter G, Marth G T, Sherry S T, McVean G, Durbin R, 1000 Genomes Project Analysis Group. 2011. The variant call format and VCFtools. Bioinformatics, 27, 2156–2158.
Davey J W, Hohenlohe P A, Etter P D, Boone J Q, Catchen J M, Blaxter M L. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12, 499-510.
Ding Y, Wang Y, Xu J, Jiang F, Li W, Zhang Q, Yang L, Zhao Z, Cheng B, Cao N, Gao X, Zhang X, Zou G, Yang F, Zhang L. 2024. A telomere-to-telomere genome assembly of Hongyingzi, a sorghum cultivar used for Chinese Baijiu production. The Crop Journal, 12, 2, 635–640.
Feller A, Machemer K, Braun E L, Grotewold E. 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. The Plant Journal, 66, 94-116.
Ganal M W, Durstewitz G, Polley A, Bérard A, Buckler E S, Charcosset A, Clarke J D, Graner E M, Hansen M, Joets J, Le Paslier M C, Mcmullen M D, Montalent P, Rose M, Schön C C, Sun Q, Walter H, Martin O C, Falque M. 2011. A large maize (Zea mays L.) SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE, 6, e28334.
Guo Z, Wang H, Tao J, Ren Y, Xu C, Wu K, Zou C, Zhang J, Xu Y. 2019. Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize. Molecular Breeding, 39, 37.
Guo Z, Yang Q, Huang F, Zheng H, Sang Z, Xu Y, Zhang C, Wu K, Tao J, Prasanna B M. 2021. Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip. Plant Communications, 2, 100230.
Hossain M S, Islam M N, Rahman M M, Mostofa M G, Khan M A R. 2022. Sorghum: A prospective crop for climatic vulnerability, food and nutritional security. Journal of Agriculture and Food Research, 8, 100300.
Kim D, Paggi J M, Park C, Bennett C, Salzberg S L. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37, 907–915.
Krueger R J. 2007. Flavonoids: Chemistry, biochemistry and applications. Economic Botany, 61, 101.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
Li X, Li X, Fridman E, Tesso T T, Yu J. 2015. Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis. Proceedings of the National Academy of Sciences of the United States of America, 112, 11823-11828.
Liu Y, Hou H, Jiang X, Wang P, Dai X, Chen W, Gao L, Xia T. 2018. A WD40 repeat protein from Camellia sinensis regulates anthocyanin and proanthocyanidin accumulation through the formation of MYB–bHLH–WD40 ternary complexes. International Journal of Molecular Sciences, 19, 1686.
Mace E S, Tai S, Gilding E K, Li Y, Prentis P J, Bian L, Campbell B C, Hu W, Innes D J, Han X, Cruickshank A, Dai C, Frere C, Zhang H, Hunt C H, Wang X, Shatte T, Wang M, Su Z, Li J, et al. 2013. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Nature Communication, 4, 2320.
Martin W G, Gregor D, Andreas P, Aurélie B, Edward S B, Alain C, Joseph D C, Eva-Maria G, Mark H, Johann J, Marie-Christine L P, Michael D M, Pierre M, Mark R, Chris-Carolin S, Qi S, Hildrun W, Olivier C M, Matthieu F. 2011. A large maize (Zea mays L.) SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE, 6, e28334
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo M A. 2010. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297–1303.
Meena K, Visarada K, Meena D. 2022. Sorghum bicolor (L.) Moench a multifarious crop-fodder to therapeutic potential and biotechnological applications: A future food for the millennium. Future Foods, 6, 100188.
Morris G P, Ramu P, Deshpande S P, Hash C T, Shah T, Upadhyaya H D, Riera-Lizarazu O, Brown P J, Acharya C B, Mitchell S E. 2013. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proceedings of the National Academy of Sciences of the United States of America, 110, 453-458.
Mwamahonje A, Eleblu J S Y, Ofori K, Feyissa T, Deshpande S, Garcia-Oliveira A L, Bohar R, Kigoni M, Tongoona P. 2021. Introgression of QTLs for drought tolerance into farmers’ preferred sorghum varieties. Agriculture, 11, 883.
Nan W, Yibing Y, Hui W, Diansi Y, Yubo L, Ao Z, Manje G, Sudha K N, Zhuanfang H, Yanli L, Felix S V, Boddupalli M P, Xinhai L, Xuecai Z. 2020. Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding. Scientific Reports, 10, 16308.
Ni D, Kong X, Sun C, Ye X, Lin L, Wang H, Wang L. 2019. Molecular structure and gelatinization characteristics of starch from Hongyingzi sorghum. China Brewing, 38, 75-79.
Prasad V R, Govindaraj M, Djanaguiraman M, Djalovic I, Shailani A, Rawat N, Singla-Pareek S L, Pareek A, Prasad P V. 2021. Drought and high temperature stress in sorghum: Physiological, genetic, and molecular insights and breeding approaches. International Journal of Molecular Sciences, 22, 9826.
Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney R K, He Z. 2017. Crop breeding chips and genotyping platforms: Progress, challenges, and perspectives. Molecular Plant, 10, 1047-1064.
Si Z, Jin S, Li J, Han Z, Li Y, Wu X, Ge Y, Fang L, Zhang T, Hu Y. 2022. The design, validation, and utility of the “ZJU CottonSNP40K” liquid chip through genotyping by target sequencing. Industrial Crops and Products, 188, 115629.
Silva-Junior O B, Grattapaglia D. 2015. Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of E ucalyptus grandis. New Phytologist, 208, 830-845.
Sun C, Dong Z, Zhao L, Ren Y, Zhang N, Chen F. 2020. The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat. Plant Biotechnology Journal, 18, 1354–1360.
Taylor J R. 2019. Sorghum and millets: Taxonomy, history, distribution, and production. Sorghum and Millets, doi: 10.1016/B978-0-12-811527-5.00001-0.
Tian H, Yang Y, Yi H, Xu L, He H, Fan Y, Wang L, Ge J, Liu Y, Wang F, Zhao J. 2021. New resources for genetic studies in maize (Zea mays L.): A genome-wide Maize6H-60K single nucleotide polymorphism array and its application. The Plant Journal, 105, 1113–1122.
Wang D, Rianti W, Gálvez F, Van Der Putten P E, Struik P C, Yin X. 2022. Estimating photosynthetic parameter values of rice, wheat, maize and sorghum to enable smart crop cultivation. Crop and Environment, 1, 119-132.
Wang J, Zhang Z. 2021. GAPIT version 3: Boosting power and accuracy for genomic association and prediction. Genomics, Proteomics & Bioinformatics, 19, 629–640.
Wu Y, Guo T, Mu Q, Wang J, Li X, Wu Y, Tian B, Wang M L, Bai G, Perumal R, Trick H N, Bean S R, Dweikat I M, Tuinstra M R, Morris G, Tesso T T, Yu J, Li X. 2019. Allelochemicals targeted to balance competing selections in African agroecosystems. Nature Plants, 5, 1229-1236.
Wu Y, Li X, Xiang W, Zhu C, Lin Z, Wu Y, Li J, Pandravada S, Ridder D, Bai G, Wang M, Trick H, Bean S, Tuinstra M, Tesso T, Yu J. 2012. Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1. Proceedings of the National Academy of Sciences of the United States of America, 109, 10281-10286.
Xu Y, Yang Q, Zheng H, Xu Y, Sang Z, Guo Z, Peng H, Zhang C, Lan H, Wang Y, Wu K, Tao J, Zhang J. 2020. Genotyping by target sequencing (GBTS) and its applications. Scientia Agricultura Sinica, 53, 2983–3004. (in Chinese)
Yan J, Yu J, Shen H, Zhou L, Chen Z, Fan X, Li Q, Zhang C, Liu Q, Huang L. 2025. Creating a superior Wx allele with temperature-responsive amylose regulation and a novel transcriptional pattern in rice via CRISPR/Cas9-mediated promoter editing. Foods, 14, 1330.
Zhang L, Ding Y, Xu J, Gao X, Cao N, Li K, Feng Z, Cheng B, Zhou L, Ren M, Lu X, Bao Z, Tao Y, Xin Z, Zou G. 2022. Selection signatures in Chinese sorghum reveals its Unique liquor-making properties. Frontiers in Plant Science, 13, 923734.
Zhang L, Xu J, Ding Y, Cao N, Gao X, Feng Z, Li K, Cheng B, Zhou L, Ren M, Tao Y, Zou G. 2023. GWAS of grain color and tannin content in Chinese sorghum based on whole-genome sequencing. Theoretical and Applied Genetics, 136, 77.
Zhang Z, Xing S, Qiu A, Zhang N, Wang W, Qian C, Zhang J, Wang C, Zhang Q, Ding X. 2025. The development of a porcine 50K SNP panel using genotyping by target sequencing and its application. Journal of Integrative Agriculture, 24, 1930–1943.
Zhao Y, Adedze Y N, Dong J, Zhang R, Zheng S, Lan H, Li Y, Liu S, Xu Y, Zhang J. 2025. Optimization of commercial SNP arrays and the generation of a high-efficiency GenoBaits Peanut 10K panel. Scientific Reports, 15, 9995.
|