Barrett J C, Fry B, Maller J, Daly M J. 2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263–265.
Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. 2007. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633–2635.
Cui Y, Zhu M M, Xu Z J, Chen W F. 2020. The breeding of japonica rice in northern China: An 11-year study (2006–2016). Journal of Integrative Agriculture, 19, 1941–1946.
Duan P, Xu J, Zeng D, Zhang B, Geng M, Zhang G, Huang K, Huang L, Xu R, Ge S, Qian Q, Li Y. 2017. Natural variation in the promoter of GSE5 contributes to grain size diversity in rice. Molecular Plant, 10, 685–694.
Fukuda M, Kawagoe Y, Murakami T, Washida H, Sugino A, Nagamine A, Okita T W, Ogawa M, Kumamaru T. 2016. The dual roles of the Golgi transport 1 (GOT1B): RNA localization to the cortical endoplasmic reticulum and the export of proglutelin and α-globulin from the cortical ER to the Golgi. Plant and Cell Physiology, 57, 2380–2391.
Kang H G, Park S, Matsuoka M, An G. 2005. White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C4-type pyruvate orthophosphate dikinase gene (OsPPDKB). Plant Journal, 42, 901–911.
Lanning S B, Siebenmorgen T J, Counce P A, Ambardekar A A, Mauromoustakos A. 2011. Extreme nighttime air temperatures in 2010 impact rice chalkiness and milling quality. Field Crops Research, 124, 132–136.
Li H, Zhang R Y, Dai C J, Lan J. 2013. Comparison of rice quality differences in three provinces in Northeast China. China Rice, 19, 18–22. (in Chinese)
Li X J, Zhang Y F, Hou M, Sun F, Shen Y, Xiu Z H, Wang X, Chen Z L, Sun S S M, Small I, Tan B C. 2014. Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize (Zea mays) and rice (Oryza sativa). Plant Journal, 79, 797–809.
Li Y B, Fan C C, Xing Y Z, Yun P, Luo L J, Yan B, Peng B, Xie W B, Wang G W, Li X H, Xiao J H, Xu C G, He Y Q. 2014. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nature Genetics, 46, 398–404.
Liu D, Wang J Y, Wang X X, Yang X L, Sun J, Chen W F. 2015. Genetic diversity and elite gene introgression reveal the japonica rice breeding in northern China. Journal of Integrative Agriculture, 14, 811–822.
Matsushima R, Maekawa M, Kusano M, Kondo H, Fujita N, Kawagoe Y, Sakamoto W. 2014. Amyloplast-localized SUBSTANDARD STARCH GRAIN4 protein influences the size of starch grains in rice endosperm. Plant Physiology, 164, 623–636.
Misra G, Anacleto R, Badoni S, Butardo V, Molina L, Graner A, Demont M, Morell M K, Sreenivasulu N. 2019. Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice. Journal of Experimental Botany, 19, 5115–5130.
NY/T 593-2013. 2013. Agricultural Industry Standard of the People’s Republic of China: Cooking Rice Variety Quality. Ministry of Agriculture of the People’s Republic of China. (in Chinese)
Qiu X, Pang Y, Yuan Z, Xing D, Xu J, Dingkuhn M, Li Z, Ye G. 2015. Genome-wide association study of grain appearance and milling quality in a worldwide collection of indica rice germplasm. PLoS ONE, 10, 1–25.
Shar T, Sheng Z H, Ali U, Fiaz S, Wei X J, Xie L H, Jiao G A, Ali F, Shao G N, Hu S K, Hu P S, Tang S Q. 2020. Mapping quantitative trait loci associated with starch paste viscosity attributes by using double haploid populations of rice (Oryza sativa L.). Journal of Integrative Agriculture, 19, 1691–1703.
Shi Y Y, Guo E J, Zhang Z T, Zhu X, Yang X G. 2020. Spatial-temporal characteristics of agricultural climate resources and sterile-type chilling injury in rice growing season in three provinces of Northeast China. Chinese Journal of Applied Ecology, 31, 1625–1635. (in Chinese)
Si L, Chen J, Huang X, Gong H, Luo J, Hou Q, Zhou T, Lu T, Zhu J, Shangguan Y, Chen E, Gong C, Zhao Q, Jing Y, Zhao Y, Li Y, Cui L, Fan D, Lu Y, et al. 2016. OsSPL13 controls grain size in cultivated rice. Nature Genetics, 48, 447–456.
Siebenmorgen T J, Grigg B C, Lanning S B. 2013. Impacts of preharvest factors during kernel development on rice quality and functionality. Annual Review of Food Science and Technology, 4, 101–115.
Tamba C L, Zhang Y M. 2018. A fast mrMLM algorithm for multi-locus genome-wide association studies. bioRxiv. [2020-10-18]. https://doi.org/10.1101/341784.
Tan Y F, Sun M, Xing Y Z, Hua J P, Sun X L. 2001. Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid. Theoretical and Applied Genetics, 103, 1037–1045.
Wang M, Li W, Fang C, Xu F, Liu Y, Wang Z, Yang R, Zhang M, Liu S, Lu S, Lin T, Tang J, Wang Y, Wang H, Lin H, Zhu B, Chen M, Kong F, Liu B, et al. 2018. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nature Genetics, 50, 1435–1441.
Wang S B, Feng J Y, Ren W L, Huang B, Zhou L, Wen Y J, Zhang J, Dunwell J M, Xu S, Zhang Y M. 2016. Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Scientific Reports, 6, 19444.
Wang X, Pang Y, Wang C, Chen K, Zhu Y, Shen C, Ali J, Xu J, Li Z. 2017. New candidate genes affecting rice grain appearance and milling quality detected by genome-wide and gene-based association analyses. Frontiers in Plant Science, 7, 1998.
Wang Y, Liu F, Ren Y, Wang Y, Liu X, Long W, Wang D, Zhu J, Zhu X, Jing R, Wu M, Hao Y, Jiang L, Wang C, Wang H, Bao Y, Wan J. 2016. GOLGI TRANSPORT 1B regulates protein export from the endoplasmic reticulum in rice endosperm cells. Plant Cell, 28, 2850–2865.
Wei X, Jiang L, Xu J, Zhang W, Lu G. 2008. Genetic analyses of heading date of japonica rice cultivars from Northeast China. Field Crops Research, 107, 147–154.
Wen Y J, Zhang H, Ni Y L, Huang B, Zhang J, Feng J Y, Wang S B, Dunwell J M, Zhang Y M, Wu R. 2018. Methodological implementation of mixed linear models in multi-locus genome-wide association studies. Briefings in Bioinformatics, 19, 700–712.
Xiao N, Gao Y, Qian H, Gao Q, Wu Y, Zhang D, Zhang X, Yu L, Li Y, Pan C, Liu G, Zhou C, Jiang M, Huang N, Dai Z, Liang C, Chen Z, Chen J, Li A. 2018. Identification of genes related to cold tolerance and a functional allele that confers cold tolerance. Plant Physiology, 177, 1108–1123.
Xin F, Xiao X, Dong J, Zhang G, Zhang Y, Wu X, Li X, Zou Z, Ma J, Du G, Doughty R B, Zhao B, Li B. 2020. Science of the total environment large increases of paddy rice area, gross primary production, and grain production in Northeast China during 2000–2017. Science of the Total Environment, 711, 135183.
Xu Q, Yuan X, Wang S, Feng Y, Yu H, Wang Y, Yang Y, Wei X. 2016. The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis. BMC Genetics, 17, 53.
Xu Z J, Shao G J, Han Y, Zhang X J, Quan C Z, Pan G J, Chen W F. 2006. A Preliminary study on yield and quality of rice and their relationship with panicle characters in Northeast Region of China. Acta Agronomica Sinica, 32, 1878–1883. (in Chinese)
Yang Y, Xu X, Zhang M, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Wei X. 2020. Genetic basis dissection for eating and cooking qualities of japonica rice in Northeast China. Agronomy, 10, 423.
Ye J, Niu X, Yang Y, Wang S, Xu Q, Yuan X. 2018. Alleles control heading date and yield potential of japonica rice in Northeast China plant materials and growing conditions. Frontiers in Plant Science, 9, 35.