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Summary  The cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene  OsHIPL1 , which encodes hedgehog‐interacting protein‐like 1 protein as a causal gene of the major QTL  qSV3  for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing (RNA‐seq) revealed that the ABA‐related genes were involved in the  OsHIPL1  regulation of seed vigour in rice. The higher levels of endogenous ABA were measured in germinating seeds of  OsHIPL1  mutants and NIL‐ qsv3  line compared to IR26 plants, with two up‐regulated ABA biosynthesis genes ( OsZEP  and  OsNCED4 ) and one down‐regulated ABA catabolism gene  OsABA8ox3 . The expression of  abscisic acid‐insensitive 3  ( OsABI3 ),  OsABI4  and  OsABI5  was significantly up‐regulated in germinating seeds of  OsHIPL1  mutants and NIL‐ qsv3  line compared to IR26 plants. These results indicate that the regulation of seed vigour of  OsHIPL1  may be through modulating endogenous ABA levels and altering  OsABIs  expression during seed germination in rice. Meanwhile, we found that OsHIPL1 interacted with the aquaporin OsPIP1;1, then affected water uptake to promote rice seed germination. Based on analysis of single‐nucleotide polymorphism data of rice accessions, we identified a Hap1 haplotype of  OsHIPL1  that was positively correlated with seed germination. Our findings showed novel insights into the molecular mechanism of  OsHIPL1  on seed vigour.

OsHIPL1 , a hedgehog‐interacting protein‐like 1 protein, increases seed vigour in rice