|
Andrews S. 2010. FastQC: A quality control tool for high throughput
sequence data. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc
Bai W Q, Yang Z Y, Yu X C, Huang S X, Wang Y F, Jing Y X, Zhang Y W, Sun
J Q. 2025. Wheat TaPKL genes regulate pre-harvest sprouting and
yield-related traits. Journal of Genetics and Genomics, 52, 1148-1150.
Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for
Illumina sequence data. Bioinformatics, 30, 2114-2120.
Bradbury P J, Zhang Z W, 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.
Chang S, Chen Y X, Jia S H, Li Y H, Liu K, Lin Z H, Wang H M, Chu Z L,
Liu J, Xi C, Zhao H P, Han S C, Wang Y D. 2020. Auxin apical dominance governed
by the OsAsp1-OsTIF1 complex determines distinctive rice caryopses development
on different branches. Public Library of Science Genetics, 16, e1009157.
Chen H Q, Zhang Z G, Ni E D, Lin J W, Peng G Q, Huang J L, Zhu L Y, Deng
L, Yang F F, Luo Q, Sun W, Liu Z L, Zhuang
C X, Liu Y G, Zhou H. 2020. HMS1 interacts with HMS1I to regulate very-long-chain fatty acid
biosynthesis and the humidity-sensitive genic male sterility in rice (Oryza sativa). New Phytologist, 225,
2077-2093.
Chun Y, Fang J J, Savelieva E M, Lomin S N, Shang J Y, Sun Y L, Zhao J
F, Kumar A, Yuan S J, Yao X F, Liu C M, Arkhipov D V, Romanov G A, Li X Y.
2023. The cytokinin receptor OHK4/OsHK4 regulates inflorescence architecture in
rice via an IDEAL PLANT ARCHITECTURE1/WEALTHY
FARMER'S PANICLE-mediated positive feedback circuit. The Plant Cell, 36, 40-64.
Dievart A, Gottin C, Périn C, Ranwez V, Chantret N. 2020. Origin and
diversity of plant receptor-like kinases. Annual Review of Plant Biology, 71, 131-156.
Du Y, Wu Q, Lu X, Jin X M,
Sun J S, Chen J Y, Guan Z R, Zhao Q, Wu H M, Wang H, Zhang M X, Zhao Y, An Y R,
Li S S, Guo B J, Li M, Guo Y. 2025. Dissecting the genetic architecture of
microelement accumulation in wheat grains through genome-wide association study. Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.04.031.
Guo B J, Jin X M, Chen J C, Xu H Y, Zhang M X, Lu X, Wu R G, Zhao Y, Guo
Y, An Y R, Li S S. 2022. ATP-dependent DNA helicase (TaDHL), a novel
reduced-height (Rht) gene in wheat. Genes, 13, 979.
Guo T, Lu Z Q, Shan J X, Ye W W, Dong N Q, Lin H X. 2020. ERECTA1 acts upstream of the OsMKKK10-OsMKK4-OsMPK6 cascade to control spikelet number
by regulating cytokinin metabolism in rice. The Plant Cell, 32, 2763-2779.
Guo Y, Liu L L, Shi X Y, Yu P Y, Zhang C, Liu Q P. 2024. Overexpression
of the RAV transcription factor OsAAT1 confers
enhanced arsenic tolerance by modulating auxin hemostasis in rice. Journal of Agricultural and Food Chemistry, 72, 24576-24586.
Hafeez A N, Chartrain L, Feng C, Cambon F, Clarke M, Griffiths S, Hayta S, Jiang M, Keller B, Kirby R, Kolodziej M C, Powell O R, Smedley M A, Steuernagel B, Xian W F, Wingen L U, Cheng S F, Saintenac C, Wulff B B H, Brown J K M. 2025. Septoria tritici blotch resistance gene Stb15 encodes a lectin receptor-like kinase. Nature Plants, 11, 410-420.
Hao X Y, Yu T F, Peng C J, Fu Y H, Fang Y H, Li Y, Xu Z S, Chen J, Dong H B, Ma Y Z, Xu W G. 2025. Somatic embryogenetic receptor kinase TaSERL2 regulates heat stress tolerance in wheat by influencing TaBZR2 protein stability and transcriptional activity. Plant Biotechnology Journal, 23, 2537-2553.
Ikeda-Kawakatsu K, Maekawa M, Izawa T,
Itoh J I, Nagato Y. 2012. ABERRANT PANICLE ORGANIZATION 2/RFL, the rice ortholog of Arabidopsis LEAFY, suppresses the transition from inflorescence meristem to floral meristem through interaction with APO1. The Plant Journal, 69, 168-180.
The International Wheat Genome Sequencing Consortium (IWGSC). 2018. Shifting
the limits in wheat research and breeding using a fully annotated reference
genome. Science, 361, 661-661.
Kim D H, Langmead B, Salzberg S L. 2015. HISAT: A fast spliced aligner
with low memory requirements. Nature Methods, 12, 357-360.
Kong X C, Wang F, Geng S F, Guan J T, Tao S, Jia M L, Sun G L, Wang Z Y,
Wang K, Ye X G, Ma J, Liu D C, Wei Y M, Zheng Y L, Fu X D, Mao L, Lan X J, Li A
L. 2022. The wheat AGL6-like MADS-box gene is a master regulator for floral organ identity
and a target for spikelet meristem development manipulation. Plant Biotechnology Journal, 20, 75-88.
Kong X C, Wang F, Wang Z Y, Gao X H, Geng S F, Deng Z Y, Zhang S, Fu M
X, Cui D D, Liu S S, Che Y Q, Liao R Y, Yin L J, Zhou P, Wang K, Ye X G, Liu D
C, Fu X D, Mao L, Li A L. 2023. Grain yield improvement by genome
editing of TaARF12 that decoupled peduncle and rachis development
trajectories via differential regulation of gibberellin signalling in wheat. Plant Biotechnology Journal, 21, 1990-2001.
Kuzay S, Xu Y F, Zhang J L, Katz A, Pearce S, Su Z Q, Fraser M, Anderson
J A, Brown-Guedira G, DeWitt N, Haugrud A P, Faris J D, Akhunov E, Bai G H,
Dubcovsky J. 2019. Identification of a candidate gene for a QTL for spikelet
number per spike on wheat chromosome arm 7AL by high-resolution genetic
mapping. Theoretical and Applied Genetics, 132, 2689-2705.
Lease K A, Wen J Q, Li J, Doke J T, Liscum E, Walker J C. 2001. A mutant Arabidopsis heterotrimeric G-protein beta subunit affects leaf, flower,
and fruit development. The Plant Cell, 13, 2631-2641.
Lee S K, Shim S H, Eom J S, Cho J I, Kwak J U, Eom S C, Jeon J S. 2024.
Cell wall invertases from maternal tissues modulate sucrose flux in apoplastic
pathways during rice anther and seed development. International Journal of Molecular Sciences, 25, 11557.
Li H, Durbin R. 2009. Fast and
accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
Li H H, Ye G Y, Wang J K. 2007. A modified algorithm for the improvement
of composite interval mapping. Genetics, 175, 361-374.
Li Q H, Brown J B, Huang H Y, Bickel P J. 2011. Measuring
reproducibility of high-throughput experiments. Annals of Applied Statistics, 5, 1752-1779.
Li X P, Zhang J J, Shi H Y, Li B, Li J. 2022. Rapid responses: Receptor-like kinases directly regulate the functions
of membrane transport proteins in plants. Journal of Integrative Plant Biology, 64,
1303-1309.
Li Y P, Li L, Zhao M C, Guo L, Guo X X, Zhao D, Batool A, Dong B D, Xu H
X, Cui S J, Zhang A M, Fu X D, Li J M, Jing R L, Liu X G. 2021. Wheat FRIZZY PANICLE activates VERNALIZATION1-A and HOMEOBOX4-A to regulate spike development in wheat. Plant Biotechnology Journal, 19, 1141-1154.
Liang J H, Lu L, Zhou H L, Fang J B,
Zhao Y F, Hou H N, Chen L Z, Cao C, Yang D W, Diao Z J, Tang D Z, Li S P. 2024.
Receptor-like kinases OsRLK902-1 and OsRLK902-2 form immune complexes with
OsRLCK185 to regulate rice blast resistance. Journal of Experimental Botany, 75, 1565-1579.
Liu H, Shi Z P, Han G H, Zhang J P, Gu T T, Wang J, Yan H W, Xing L X,
Li L H, An D G. 2024. A rare natural variation in TaFT-D2 underlies QTss.cas-3D associated with
increased total spikelet number per spike in wheat. The Crop Journal, 12,
1727-1734.
Liu Q, Wang C, Jiao X Z, Zhang H W, Song L L, Li Y X, Gao C X, Wang K J.
2019. Hi-TOM: A platform for high-throughput tracking of mutations induced by
CRISPR/Cas systems. Science China-Life Sciences, 62, 1-7.
Liu S Y, Xie L N, Wu H B, Xu D G, Che R, Tian W F, Liu B Y, Chao Y H,
Zhang Y, Xia X C, He Z H, Cao S H. 2025. TaIAA10-6D orchestrates processing quality and grain yield by modulating glutenin/gliadin
ratio and plant morphogenesis in wheat. The Crop Journal, 13, 1460-1469.
Liu Y Y, Chen J, Yin C B, Wang Z Y, Wu H, Shen K C, Zhang Z L, Kang L P,
Xu S, Bi A Y, Zhao X B, Xu D X, He Z H, Zhang X Y, Hao C Y, Wu J H, Gong Y, Yu
X C, Sun Z W, Ye B T, et al. 2023. A
high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in
wheat. Genome Biology, 24, 196.
Liu Z J, Hu Y Z, Du A P, Yu L, Fu X Y, Wu C L, Lu L X, Liu Y X, Wang S
H, Huang W Z, Tu S B, Ma X R, Li H. 2022. Cell wall matrix polysaccharides
contribute to salt–alkali tolerance in rice. International Journal of Molecular Sciences, 23, 15019.
Love M I, Huber W, Anders S. 2014. Moderated estimation of fold change
and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550.
Miao Y L, Xun Q, Taji T, Tanaka K,
Yasuno N, Ding C Q, Kyozuka J. 2022. ABERRANT PANICLE ORGANIZATION2 controls multiple steps in
panicle formation through common direct-target genes. Plant Physiology, 189,
2210-2226.
Niu E B, Zhang Y B, Xu H H, Xu B L, Liang Q L, Li H X, Wang J H. 2025. A G-type lectin receptor-like kinase TaSRLK confers wheat resistance to stripe rust by regulating the reactive oxygen species signaling pathway. Stress Biology, 5, 37.
Van Ooijen J W. 2009. Mapqtl 6: Software for the Mapping of Quantitative
Trait Loci in Experimental Populations of Diploid Species. The Netherlands: Kyazma BV, Wageningen.
Peng B, Zhang Q X, Liu Y, Zhao Q, Zhao J H, Zhang Z G, Sun X Y, Peng J,
Sun Y F, Song X H, Guo G Y, Huang Y Q, Pang R
H, Zhou W, Wang Q X. 2024. OsAAP8 mutation leads to significant
improvement in the nutritional quality and appearance of rice grains. Molecular Breeding, 44, 34.
Saintenac C, Lee W S, Cambon F, Rudd J J, King R C, Marande W, Powers S J, Bergès H, Phillips A L, Uauy C, Hammond-Kosack K E, Langin T, Kanyuka K. 2018. Wheat receptor-kinase-like protein Stb6 controls gene-for-gene resistance to fungal pathogen Zymoseptoria tritici. Nature Genetics, 50, 368-374.
Sakuma S, Golan G, Guo Z F, Ogawa T, Tagiri A, Sugimoto K, Bernhardt N,
Brassac J, Mascher M, Hensel G, Ohnishi S, Jinno H, Yamashita Y, Ayalon I,
Peleg Z, Schnurbusch T, Komatsuda T. 2019. Unleashing floret fertility in wheat
through the mutation of a homeobox gene. Proceedings of the National Academy of Sciences of the United States of America, 116, 5182-5187.
Shen L P, Zhang L L, Yin C B, Xu X W, Liu Y Y, Shen K C, Wu H, Sun Z W,
Wang K, He Z H, Zhang X Y, Hao C Y, Hou J,
Bi A Y, Zhao X B, Xu D X, Ye B T, Yu X C, Wang Z Y, Liu D N, et al. 2024. The wheat sucrose synthase
gene TaSus1 is a determinant of grain number per spike. The Crop Journal, 12,
295-300.
Shen Q W, Zhan X Q, Yang P, Li J, Chen J, Tang B, Wang X M, Hong Y Y.
2019. Dual activities of plant cGMP-Dependent protein kinase and its roles in
gibberellin signaling and salt stress. The Plant Cell, 31, 3073-3091.
Shiu S H, Bleecker A B. 2001. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proceedings of the National Academy of Sciences of the United States of America, 98, 10763-10768.
Sun Z J, Zhang M X, An Y R, Han X, Guo B J, Lv G D,
Zhao Y, Guo Y, Li S S. 2022. CRISPR/Cas9-mediated disruption of Xylanase inhibitor protein (XIP) gene
improved the dough quality of common wheat. Frontiers in Plant Science, 13, 811668.
Voss-Fels K P, Keeble-Gagnère G, Hickey L T, Tibbits J, Nagornyy S,
Hayden M J, Pasam R K, Kant S, Friedt W, Snowdon R J, Appels R, Wittkop B.
2019. High-resolution mapping of rachis nodes per rachis, a critical
determinant of grain yield components in wheat. Theoretical and Applied Genetics, 132, 2707-2719.
Wang J B, Zhang Z W. 2021. GAPIT version 3: Boosting power and accuracy
for genomic association and prediction. Genomics, Proteomics & Bioinformatics, 19, 629-640.
Wang L, Ming L C, Liao K Y, Xia C J, Sun S Y, Chang Y, Wang H K, Fu D B,
Xu C H, Wang Z J, Li X, Xie W B, Ouyang Y D, Zhang Q L, Li X H, Zhang Q H, Xiao
J H, Zhang Q F. 2021. Bract suppression regulated by the
miR156/529-SPLs-NL1-PLA1 module is required for the transition from vegetative
to reproductive branching in rice. Molecular Plant, 14, 1168-1184.
Wang M L, Lu X D, Xu G Y, Yin X M, Cui Y C, Huang L F, Rocha P S C F,
Xia X J. 2016. OsSGL, a novel pleiotropic stress-related gene enhances
grain length and yield in rice. Scientific Reports, 6, 38157.
Xu H Y, Dong J J, Meng X R, Jiang H J, Ding G S, Wang Z X, Wang F X,
Wang Y M, Wu M H, Ma L J, Miao G C, Qin R, Zhao C H, Sun H, Cui F, Wu Y Z.
2025. TaHAL3-7A increases grain yield by enhancing
photosynthetic pigment content in
wheat (Triticum aestivum L.). The Plant Journal, 122, e70274.
Xu J M, Wang C L, Wang F J, Liu Y P, Li M, Wang H J, Zheng Y H, Zhao K
J, Ji Z Y. 2023. PWL1, a G-type lectin receptor-like kinase, positively
regulates leaf senescence and heat tolerance but negatively regulates
resistance to Xanthomonas oryzae in rice. Plant Biotechnology Journal, 21, 2525-2545.
Xu X S, Lin H Q, Zhang J L, Burguener G, Paraiso F, Li K, Tumelty C, Li
C X, Liu Y C, Dubcovsky J. 2025. Spatial and single-cell expression analyses
reveal complex expression domains in early wheat spike development. Genome Biology, 26, 352.
Yamaji N, Yoshioka Y, Huang S, Miyaji T, Sasaki A, Ma J F. 2024. An
oligo peptide transporter family member, OsOPT7, mediates xylem unloading of Fe
for its preferential distribution in rice. New Phytologist, 242, 2620-2634.
Yan Q, Pang Y L, Lu Y, Zhu H Q, Lu Y, Li J Y, Sun Z N, Li Z Y, Zhao H L,
Li G Y, Wu Y Y, Liu S B. 2025. qSL2B/TaeEF1A regulates spike development
and grain number in wheat. Crop Journal, 13, 900-908.
Yao Y Y, Guo W L, Gou J Y, Hu Z R, Liu J, Ma J, Zong Y, Xin M M, Chen W,
Li Q, Wang Z H, Zhang R J, Uauy C, Baloch F S, Ni Z F, Sun Q X. 2025. Wheat
2035: Integrating pan-omics and advanced biotechnology for future wheat design. Molecular Plant, 18,
272-297.
Yin
Z Y, Liu J D, Dou D L. 2024. RLKdb: A comprehensively curated database of plant
receptor-like kinase families. Molecular Plant, 17, 513-515.
Yu J, Xuan W, Tian Y L, Fan L, Sun J, Tang W J, Chen G M, Wang B X, Liu
Y, Wu W, Liu X L, Jiang X Z, Zhou C, Dai Z Y, Xu D Y, Wang C M, Wan J M. 2021.
Enhanced OsNLP4-OsNiR cascade confers nitrogen use efficiency by
promoting tiller number in rice. Plant Biotechnology Journal, 19, 167-176.
Yuan Y Y, Gao M G, Zhang M X, Zheng H H, Zhou X W, Guo Y, Zhao Y, Kong F
M, Li S S. 2017. QTL mapping for phosphorus
efficiency and morphological traits at seedling and maturity stages in wheat. Frontiers in Plant Science, 8, 614.
Zhang H H, Chen C H, Li L L, Tan X X, Wei Z Y, Li Y J, Li J M, Yan F,
Chen J P, Sun Z T. 2021. A rice LRR receptor-like protein associates with its
adaptor kinase OsSOBIR1 to mediate plant immunity against viral infection. Plant Biotechnology Journal, 19, 2319-2332.
Zhang H Z, Ma L T, Zhai Y H, Wang H, Niu M S, Zhang M X, Guo Y, An Y R,
Li S S, Zhao Y. 2025. A phosphatidylinositol 4-kinase alpha (PI4KA) gene
reduces plant height of common wheat. Genes, 962, 149556.
Zhang J H, Lin Q B, Wang X, Shao J L, Ren Y L, Liu X, Feng M, Li S, Sun
Q, Luo S, Liu B J, Xing X X, Chang Y Q, Cheng Z J, Wan J M. 2025. The DENSE AND
ERECT PANICLE1-GRAIN NUMBER ASSOCIATED module enhances rice yield by repressing CYTOKININ OXIDASE 2 expression. The Plant Cell, 37, koae309.
Zhang M X. 2019. Construction of genetic
map for unigenes and QTL mapping for nitrogen use efficiency related traits in
wheat. Ph D thesis, Shandong
Agriculture University, Tai’an, China.
Zhang M X, Gao M G, Zheng H H, Yuan Y Y, Zhou X W, Guo Y, Zhang G Z,
Zhao Y, Kong F M, An Y R, Li S S. 2019. QTL mapping for nitrogen use efficiency
and agronomic traits at the seedling and maturity stages in wheat. Molecular Breeding, 39, 71.
Zhang M X, Han X, Wang H,
Sun J S, Guo B J, Gao M G, Xu H Y, Zhang G Z, Li H N, Cao X F, Li N N, Xu Y R,
Wu Q, Wang C Y, Zhang G H, Yuan Y P, Man J X, Pu Y Y, Lv G D, Qu C Y, et al. 2024. Efficient cloning of genes
for wheat yield component traits from QTLs via sequencing of the RIL
population. bioRxiv. https://doi.org/10.1101/2024.02.22.574000
Zhang N, Li S G, Sun Z P, Dai J J, Zhang S Y, Chen D Y, Zhao L, Jia A L, Chen F. 2025. A lectin receptor-like kinase TaSRK that is deacetylated by TaHDA9 regulates wheat grain length by mediating the photosystem II protein TaPsbO. Science Bulletin, 70, 3120-3124.
Zhang S J, Zhang R Z, Gao J, Song G Q, Li J H, Li W, Qi Y P, Li Y L, Li
G Y. 2021. CRISPR/Cas9-mediated genome editing for wheat grain quality
improvement. Plant Biotechnology Journal, 19, 1684-1686.
Zhang X R. 1998. Leucine-rich repeat receptor-like kinases in plants. Plant Molecular Biology Reporter, 16, 301-311.
Zhang X Y, Jia H Y, Li T, Wu J Z,
Nagarajan R, Lei L, Powers C, Kan C C, Hua W, Liu Z Y, Chen C, Carver B F, Yan
L L. 2022. TaCol-B5 modifies spike architecture and enhances grain yield
in wheat. Science, 376,
180-183.
Zhang Y, Liu T, Meyer C A,
Eeckhoute J, Johnson D S, Bernstein B E, Nusbaum C N, Myers R M, Brown M, Li W,
Liu X S. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biology, 9, R137.
|